# HG changeset patch
# User artbio
# Date 1521323038 14400
# Node ID b3fe7c4ca5aa2698367d8aa821437dc1ff0c0a52

planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d

diff -r 000000000000 -r b3fe7c4ca5aa README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Sat Mar 17 17:43:58 2018 -0400
@@ -0,0 +1,30 @@
+Trinity memory usage
+====================
+
+As described on the official Trinity website
+`FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_,
+trinity requires a large amount of memory to perform the assembly: "roughly
+~1G of RAM per 1M reads to be assembled"
+
+By default, this tool is configured to limit the memory consumption to 1G.
+You might need to lower this limit if the machine(s) executing the jobs have less memory available.
+If you have a lot of reads to assemble and a machine with enough memory, you can increase it.
+In both cases, you can set the GALAXY_MEMORY_MB environmental variable in the destination section of the job_conf.xml file::
+
+    <?xml version="1.0"?>
+    <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
+    <job_conf>
+        <plugins>
+            <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
+        </plugins>
+        <handlers>
+            <handler id="main"/>
+        </handlers>
+        <destinations>
+            <destination id="local" runner="local">
+                <env id="GALAXY_MEMORY_MB">1G</env>
+            </destination>
+        </destinations>
+    </job_conf>
+
+
diff -r 000000000000 -r b3fe7c4ca5aa macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sat Mar 17 17:43:58 2018 -0400
@@ -0,0 +1,39 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.4.0">trinity</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <token name="@WRAPPER_VERSION@">2.4.0</token>
+
+    <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
+        #if $pool.inputs.strand.is_strand_specific:
+            --SS_lib_type $pool.inputs.strand.library_type
+        #end if
+
+        $pool.inputs.jaccard_clip
+    </token>
+
+    <xml name="input_paired_strand_jaccard">
+        <conditional name="strand">
+            <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
+            <when value="false" />
+            <when value="true">
+                <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
+                    <option value="FR">Forward-Reverse</option>
+                    <option value="RF">Reverse-Forward</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="jaccard_clip" argument="--jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="Set if you expect high gene density with UTR overlap"/>
+    </xml>
+
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1038/nbt.1883</citation>
+        </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r b3fe7c4ca5aa test-data/norm/Trinity.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/norm/Trinity.fasta	Sat Mar 17 17:43:58 2018 -0400
@@ -0,0 +1,46 @@
+>TRINITY_DN1_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN0_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2]
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2]
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2]
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2]
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2]
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
+
diff -r 000000000000 -r b3fe7c4ca5aa test-data/norm/Trinity_paired_unmerged_1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/norm/Trinity_paired_unmerged_1.fasta	Sat Mar 17 17:43:58 2018 -0400
@@ -0,0 +1,47 @@
+>TRINITY_DN0_c0_g1_i1 len=216 path=[1:0-215] [-1, 1, -2]
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
+>TRINITY_DN1_c0_g1_i1 len=380 path=[1:0-379] [-1, 1, -2]
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN2_c0_g1_i1 len=229 path=[135:0-228] [-1, 135, -2]
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN3_c0_g1_i1 len=202 path=[1346:0-201] [-1, 1346, -2]
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g2_i1 len=669 path=[736:0-161 12:162-668] [-1, 736, 12, -2]
+GCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATT
+GTCACTCTTGTATTTGAAAAACACTTTCCGGCCACCATTGATTCTTTCCAGGATGCAGTG
+AAGTGTTTGTCTGAATTCACATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATC
+CGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTAC
+ACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCG
+ATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGC
+TTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGG
+CAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAG
+ACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGAT
+GTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAG
+CTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTA
+GAAAACGTG
+>TRINITY_DN3_c0_g3_i1 len=240 path=[519:0-239] [-1, 519, -2]
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN3_c0_g4_i1 len=279 path=[983:0-278] [-1, 983, -2]
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
diff -r 000000000000 -r b3fe7c4ca5aa test-data/raw/Trinity.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/Trinity.fasta	Sat Mar 17 17:43:58 2018 -0400
@@ -0,0 +1,46 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2]
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2]
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2]
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2]
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2]
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
+
diff -r 000000000000 -r b3fe7c4ca5aa test-data/raw/Trinity_single_unmerged_1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/Trinity_single_unmerged_1.fasta	Sat Mar 17 17:43:58 2018 -0400
@@ -0,0 +1,5 @@
+>TRINITY_DN0_c0_g1_i1 len=226 path=[1:0-225] [-1, 1, -2]
+CTTTACATCTGTACCATATACATATCCACCTGAAAACATTTTCTACATCCACTGTTATAT
+GGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCACAGTTCACAGTATGAATACAT
+TTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTTTGTTATTTTTAATATATTCAACA
+TTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGCCACCC
diff -r 000000000000 -r b3fe7c4ca5aa test-data/reads.left.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.left.fq	Sat Mar 17 17:43:58 2018 -0400
@@ -0,0 +1,400 @@
+@61DFRAAXX100204:1:100:10494:3070/1
+ACTGCATCCTGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTTT
++
+ACCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC?CCCCCCCCC@@CACCCCCACCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:100:10497:13422/1
+GTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAGGTAGGCTGATGC
++
+CCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCCCCCCCCCCCCDDCCDDCDCBDCCDDDDBADDADDB@DBBBA@
+@61DFRAAXX100204:1:100:10546:4478/1
+CTGGGCTGCAGCTAAGTTCTCTGCATCCTCCTTCTTGCTTGTGGCTGGGAAGAAGACAATGTTGTCGATGGTCTGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC7CB@CA:>AB?C=C@@@@?A@?5:88:
+@61DFRAAXX100204:1:100:10609:6818/1
+CACGTTTTCTAAGCAGTTTGTACCAGATCGTGCTAACTGCTCATTGTCTTGTTGTACACACCAGTAAAGCTGGGCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:100:10648:5988/1
+TGCTCATTGTCTTGTTGTACACACCAGTAAAGCTGGGCAAAAATATCATCCAAAAGTACATCGCTGAGAACTCCTA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCDCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:100:11486:13583/1
+CCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCAC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC
+@61DFRAAXX100204:1:100:1176:14271/1
+TCTGAATAAGTCCTGCCACCAATGTTTTTCATAAGTGTGGCCATATGTTTTCATTATTTCAAACATTACTGTTAAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCDCDCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCDBBABDB
+@61DFRAAXX100204:1:100:12152:16425/1
+CTCCGTTTTTTGAGAGTGCAACACATAGATACTGCTTGATAGCATTAATAAACATCTCATTTGTCCTGAAAACAGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:100:14680:13081/1
+GCCTGAGTGTGCAAAAATCTTCAGAGTAAGAATACCATAGTTGCTAAATATCTTTTACCATGAGCAATAATTTTTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC;CCCCCC
+@61DFRAAXX100204:1:100:16086:14019/1
+TCTGGTGCAGCTAGATGGAATACTGAGAAAATGTTCTTCCATCCTGAACGAATATTTGCAGCCTGAGAATTAACCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCBCCDDCDCC
+@61DFRAAXX100204:1:100:17458:1622/1
+GTGAAAGGTCATCTATTTTAATGGCTTGTCTTTAAAAACCCTAAGAGAGGGAGGATGTCACAGGGAGGGCTTGTCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCC5A###############################################
+@61DFRAAXX100204:1:100:17716:21197/1
+CCAGGCTTCCCGGTGACTTTCGGATGTTAGAGTGAGGAAGTAGCTCAGCGCTTCCCTGCAGACGTTTAAAAGCCTC
++
+CCCCCCCCCCCCCBCCCCCCCCC@CCCCCC@BBCCCCCCCBDB>CCCCAC@BCBBCDDBD@?BCBA@6BBB>;A;:
+@61DFRAAXX100204:1:100:19734:13092/1
+ATCATCTTGGAGACTTTTATCCACATCATGTGTTTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCA
++
+;CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCDC
+@61DFRAAXX100204:1:100:2082:1789/1
+ACGGGTGTGGTGCCAAGCATCCCTTGTTCTTGGAGGTATTGTATTCCTCTCTTTGGTTTCTTATTAAATAAATCAA
++
+CCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCADCCCDBCCCCCCCCCCDABBCCDCC@CBBBDDDD;@B?=
+@61DFRAAXX100204:1:100:2172:8797/1
+GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGGATCTTGCAGCAAATT
++
+############################################################################
+@61DFRAAXX100204:1:100:2238:12815/1
+ACCATAGTTGCTAAATATCTTTTACCATGAGCAATAATTTTTTTCTCCCTTCCCCCACCCCCAATTATAAACATTT
++
+############################################################################
+@61DFRAAXX100204:1:100:2327:5980/1
+CTCCTAAATAATTTCCATCAGTGTGGGCCACCGTGATGAGTGTTTTTATTGTGTCGATATTCTTCTGTTTCATTTC
++
+CCCCCCCCCCCCCCCCCCCCCCCCC0BBBACCCBCCCCCC=CCCCCB@B@=DC@CCDDBCC-CC@CABBBB<CCCA
+@61DFRAAXX100204:1:100:3665:17139/1
+ATACTTCTTTGGGTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAG
++
+CCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCDCBCCCCCCCCCCCCCCCCCCCCCCCCBCBCDCCCBDBA>DC
+@61DFRAAXX100204:1:100:6480:5393/1
+TGGAGACTTTTATCCACATCATGTGTTTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCAACAGTCT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCBCCCCBDCBDDADBDC
+@61DFRAAXX100204:1:100:8693:14085/1
+AGCTATTTCGTTATAAATGGCTGATAGATACTCTTCAGGGAGATCTTTACTGTCATTGATACCACGATTCATTTTA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:100:9306:14527/1
+GTAGAATGATGCGTGAGCTTTAAACCTGCTGTCACTGATCTTCAGAACTTTAGTGAGGAACAGTAACAGTAAGTTA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCBACDCCBCDCBCC
+@61DFRAAXX100204:1:100:9656:2687/1
+CTTCTAGGCAAAGAGAGGCTACTTCAGTATCATCACAGTCTTGGAGACCCACACTGAATGCAGCCAGAAAAGGTGT
++
+BBBBBBBBBBBBBBBBBBBBB>>B>;=;=7>>?>>B>>;>BB>B################################
+@61DFRAAXX100204:1:101:11219:19264/1
+TTTGCTAACTTCTTCACTCACAGTAGAAACAGAAACCAGTGGTGCTTGCTGTCTGTTATCTGAAGATCTNGGTTGA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCABCCCCCCCCCCCCCC@CBCC;DB<>>A&>99>;@
+@61DFRAAXX100204:1:101:11349:8542/1
+GGGTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAGGTANGCTGAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCAA;A'??@=@>
+@61DFRAAXX100204:1:101:11674:10443/1
+CACCCACACCCTGTCTTCAGGTGCCACGCTCATGTCATCACTTGTGTACTCCTTGAAAGCCTGCGGTCTNTCAGAC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCACCCCCCCCCCACC&AAA?AC
+@61DFRAAXX100204:1:101:1179:19106/1
+TTGGTTGAATAGAATCATGTATGTCTACAGATTTTTGTGATATTGCATCCAACGGCTTTTCACTCACAGNTGATGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCCCCCCCCCCCCCCCCCACCCCADCCBCA@'AA=@??
+@61DFRAAXX100204:1:101:12110:12654/1
+CTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATCCGGAAGAGAATGCGCAGCCCACACGCCAGGCNGCTTGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCBCCDCCBCCDCCDCBCDAD@ABBDDDAD@BABB.625'?A=:@0
+@61DFRAAXX100204:1:101:13165:4417/1
+CTGGATTATCAGTGCCAGACATCTGTGTACTGTAGCTGCCAATTCCTGATGATGATGTGGATTCTAAGGNGTTTAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA?&75:;8C
+@61DFRAAXX100204:1:101:13420:13159/1
+GGTGGATCCCCTCCTGTTGTCATCTTGACAGGCATCAGCCACAACAGATTCAGGGCACAGCAAGCCCTCNAAATGA
++
+CCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACAC&89848C
+@61DFRAAXX100204:1:101:14810:10441/1
+CAGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTCTGNAATGCA
++
+CCCCCCCCCCCCCCCCCDCCCCCCCCCCBCBCCCBBCCCCCCCBCCCDCCCCCCCDCCDCCCDCC:A?A'AAAAAC
+@61DFRAAXX100204:1:101:15025:8342/1
+GTGGGTAGGAAGCCTCTGCTGCAGGATCCTTTCACAGAGCAGAGCAATGTAAACACCAACAGAAAAACANCGGCTC
++
+CCCCCDCCCCC@CCCCCCCCCCCCCCCCCCCCCCCCCDCCCCBDBCCBCDCCCDCCDCBDACBBD=999%8====B
+@61DFRAAXX100204:1:101:15551:15592/1
+CTCCCAAAACCATGCCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATNTACATC
++
+CCCCCCCCCCCCCCCCCCCDCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA=7A'AAB?AC
+@61DFRAAXX100204:1:101:16061:6897/1
+ATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCACAGTTCACAGTATGAATACATTTCCAGTNAATCTA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCDCCCCCCCDCCCCDC=C@'ABAAAC
+@61DFRAAXX100204:1:101:16516:11581/1
+GGCCCTAAAGGTAGGCTGATGCTGTGGGAACAGCCTTTCTGCTCAATATGAGCCCAACACGCGACAGAGNCCACTG
++
+74/8588857;-84;<<<<<-88;8488+8A<286A9AA#####################################
+@61DFRAAXX100204:1:101:17825:1193/1
+ACGCTCATGTCATCACTTGTGTACTCCTTGAAAGCCTGCGGTCTATCAGACACATATTTTGCACAATGGNGAATAA
++
+BCCCCCCCCCCCCCCCDCCCCCCCCCCCC@CBCCCCCCC@CCCCCBCDCCCCCCCCCCCCCCCCCAABA&A>>??A
+@61DFRAAXX100204:1:101:2920:3823/1
+TCCATCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTNTGTTAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB'CCBC@C
+@61DFRAAXX100204:1:101:4549:18278/1
+AGGTGGATCCCCTCCTGTTGTCATCTTGACAGGCATCAGCCACAACAGATTCAGGGCACAGCAAGCCCTNAAAATG
++
+AB?BA:?B<?>:>:7;=BB=??>A>>>:+>//000BBBB@B@BBBBABBBB>B@?ABBBBBB>@############
+@61DFRAAXX100204:1:101:5059:19347/1
+TTTGGACTTGCCTTTGAAGCCTGCTTTCCACAGAGCAGTCCTCTGTTCATTGTTGGAATTAAATGCTTTNGCAAAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCC&89:79C
+@61DFRAAXX100204:1:101:5741:4886/1
+CCCACCCCCAATTATAAACATTTTATCCTTCAAAATACAGCTCTCCTGAGTTGTACTTCTCGCAGAAGCNCAGTCT
++
+CCCCCCBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'B?BAAC
+@61DFRAAXX100204:1:101:6207:10801/1
+GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGTATCTTGCANCAAATT
++
+DCCCCCCCDBCCCCCCCCCCCCCCCCCCCCCAC@CAA9AACCCCCCCC@CCCCCCCCCCB@CCCC###########
+@61DFRAAXX100204:1:101:6228:11229/1
+CAGTGATTCAAGTTTCAGTCTGTGAAAGGTCATCTATTTTAATGGCTTTTCTTTAAAAGCCCTAAGAGANTGAGTA
++
+CBCCCCCCCCCCCCC@CCBBCC@CC@<BB@C@CC@CC?CBC?C<CCC?CCC?>>:<5?/:>A?:A###########
+@61DFRAAXX100204:1:101:7284:17741/1
+CAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGNCACCCA
++
+CCCCCCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCC@'CCCCCC
+@61DFRAAXX100204:1:101:7317:19738/1
+ATGAGAATCAATATTGTACAGAAAGTTGTACAGAATTTTTTTACATAGAAAACTTTACATCTGTACCATNTACATA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCACC'AAAAA@
+@61DFRAAXX100204:1:101:7386:20759/1
+CCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTCTGAAATGCAAGTTCTACTATGNTTTCAT
++
+CCCCCCCCCCCCCCCBBCCCCCCCCCCCBCCCCCCCDCCCCCCDCCBCCCCCCDCCBBCBCCCCCCBBC)ACBA@D
+@61DFRAAXX100204:1:101:7661:3279/1
+TTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCAACAGTCTGAGGTGGCAAATATCTAAGNTGAGGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCC'@????=
+@61DFRAAXX100204:1:101:7989:14539/1
+CGTGCTCCAAGTGTGTTGCACTTGTAAAAGGTGCCTGAACATGGCTCACAGCTTCCATGAGTGCTTTAGNCGTCTT
++
+CCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCBDCCCCCCCCCABCCCCCBCCCCCCBCC=CBCCCCCCC'AA<A@C
+@61DFRAAXX100204:1:101:8630:9416/1
+GAGGGAGACAGGCGAGTAGGTGGCGGTGGGGGCGAGGAGGCGTGGATGCTAGCCGCCGTCTCCGTTAGCNTCCGTC
++
+############################################################################
+@61DFRAAXX100204:1:101:9622:17436/1
+GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGTATCTTGCANCAAATT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCBBCCCBBBB'AAA=AC
+@61DFRAAXX100204:1:102:10071:12692/1
+TGCGTGAGCTTTAAATTTAAAAGCCTCTGCTGGANTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATCC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDBCCDCCDDAC
+@61DFRAAXX100204:1:102:10556:11503/1
+TCCTGGGATTCCATTTGCTTGGATGTTTTCACTGNCACTACCATCTTCTACAGTTCCAGTGTTGCCTTCTGTACTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BBBBBCCCCCCCCCCCCCCCCCBCBCDCDCCCDBDBCAABB
+@61DFRAAXX100204:1:102:10558:14342/1
+ATGTTTTCTACCTTGGTGGATCCCCTCCTGTTGTNATCTTGACAGGCATCAGCCACAACAGATTCAGGGCACAGCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC
+@61DFRAAXX100204:1:102:12109:19420/1
+TCTGTTATCTGAAGATCTTGGTTGAATAGAATCANGTATGTCTACAGATTTTTGTGATATTGCATCTTACCAACGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'>????DCCCCCCCCCCCCC@BACCCCCCBCDCCCDCDBDDB
+@61DFRAAXX100204:1:102:12757:13134/1
+GGGATGTATTGAACCACTGCTCTCAGGACAGGAANAAACAATGCACAAGCAATTTTCTTCCTAAATAACAATTCAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC)BBBBBCCCCCCCCCCCCCCCCCC@BCCCCCCCCCCACCCCC
+@61DFRAAXX100204:1:102:13549:15464/1
+GTCCATGTACATCCGGAAGAGAATGCGCAGCCCANACGCCAGGCTGCTTGTCTCCTGTTTTAGAAGATTGGGCTTG
++
+CCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCC'CCCCCCCCCCC?CCCDCCBCCCBDCDBDDBBCADA<AC@BB
+@61DFRAAXX100204:1:102:13777:6235/1
+CGCAGGACTCACAAGGGTAAAGCAAATTAAGAACNCGTCTGTCTGCGGGTAGGAGAGGGGACGCAATCTGTCATAC
++
+############################################################################
+@61DFRAAXX100204:1:102:14960:18241/1
+GCCACGAATTTCCTAAATAATTTCCATCAGTGTGNGCCACCGTGATGAGTGTTTTTATTGTGTCGATATTCTTCTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC&CCCCCCCCCCCCCCDCCCCCB@BB@DCCCCDCBCCCCCCCC
+@61DFRAAXX100204:1:102:15063:6971/1
+CAGAAAAGGTGTCCAAGCCAACTTAAACATCGGCNTCACGTGCTCCAAGTGTGTTGCACTTGTAAAAGGTGCCTGA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'8;9;9CCCCCCC@CBCCCCCCCCCCCCCCCCDCAACBBBBC
+@61DFRAAXX100204:1:102:16420:15231/1
+GTTGTACTTCTCGCAGAAGCTCAGTCTTTACATCNATACTTCTTTGGGTAATTTCCGTACCTGCCACAGTGTGGGC
++
+CCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCC'CCCBCCCCACCCCCCDCCCDCDDDCAB@BDBBDDCBCACCB
+@61DFRAAXX100204:1:102:16908:12433/1
+CACTGATGAAATAATTCAAAAACTTTATTGACCTNTAACCTGATTAGATATGCCAGATGAGAATCAATATTGTACA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCC
+@61DFRAAXX100204:1:102:17677:10400/1
+CGCACATCTTATCCCTTCTAGGCAAAGAGAGGCTNCTTCAGTATCATCACAGTCTTGGAGACCCACACTGAATGCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC',00.-;7;<4?@>:A##########################
+@61DFRAAXX100204:1:102:17711:7491/1
+ACTCTGGACAATATCAAGTGGCTTTTCTTCATAGNCTCCATCATACAAGATATCATTTTTAGATAATGTTTCAGCT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCDCCCCBCA
+@61DFRAAXX100204:1:102:17798:2084/1
+CCTTGTTCTTGGAGGTTTTGTATTCCTCTCTTTGNTTTCTTATTAAATAAATCAATCCCTTGTTCTATTATTTCTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBB'BBBBBCCCCCCCCCCBBCCACCCCCCCCCCCCCCDCCCCCC
+@61DFRAAXX100204:1:102:18807:10059/1
+CTGCACTGGAAATATCAGATCCGTTTTCAGGCTCNGTATCATCTTGGAGACTTTTATCCACATCATGTGTTTGGGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC&CBCCCCCCCCCC@CDCCCCCCCDCDCDC@ACDBADDBB;BA
+@61DFRAAXX100204:1:102:19518:11565/1
+CCTGGGAAGAAGACAATGTTGTCGATGGTCTGGANGAGTTCCAGCTGCACAACACATTTAATCAACAGGGCAGCAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCC'BAB>BCCCBCCCCCCCDDACABCCBACCACDAD@DDBD<>C
+@61DFRAAXX100204:1:102:2639:2051/1
+CTGCCTCAGAGAGTCTACTGCAAATATGGCTACANCTTCATTAGGATTACAACCAACCTTATTAAAATGATCTCCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAA3A##########################################
+@61DFRAAXX100204:1:102:3101:2926/1
+CTTCCCAGGCACTGACTCTGCTCTCGTCCATGTANATCCGGAAGAGAATGCGCAGCCCACACGCCAGGCTGCTTGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BBBBBCCBCCCCCCCCCCCCCCCCCCC<CCCDDCAAB@B<B
+@61DFRAAXX100204:1:102:5977:14503/1
+GGGGGTTCGGCCTCGCCAGAGGTGGGACGCCAAGNCAGAAGCGCGTGAGGAATTGTGGTTTTGAAGATATCCAGGG
++
+CCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCC'CCCCCCCCCCDCACCBCBCC?CCBCCCCAACDCCCBCDCCA
+@61DFRAAXX100204:1:102:6251:21399/1
+CCCAGCTATTTCGTTATAAATGGCTGATAGATACNCTTCAGGGAGATCTTTACTGTCATTGATACCACGATTCATT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BBBBACCCCCCCCCCC@CCCDCCCCCDCDCCBCCBCDD@CC
+@61DFRAAXX100204:1:102:7093:4246/1
+CGGGTCTTGTCAGCAGGGATGTTTTCTACCTTGGNGGATCCCCTCCTGTTGTCATCTTGACAGGCATCAGCCACAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(CCCCCCCCCCB@CDCCDCCCCCCCDDDCBDDBDDBDCDABB
+@61DFRAAXX100204:1:102:7907:21314/1
+AGACACATATTTTGCACAATGGCGAATAAGTCGGNTTGCTTCCATACTTGTGTCTGGGAAAGCTGCATTACATGCG
++
+>BBB>BB>BBB<B?>?>??<99:<9:A<??0000%*000089:;<74;?8BABBBBA>B#################
+@61DFRAAXX100204:1:102:8037:6949/1
+TCTAGGTATCTTGCAGCAAATTTTTCCATTAATCNATCAATTTTCTGAGCTTCTCCTGGAAGCCGGAATCCTTCCA
++
+CCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCC(BBBBBCCCCCCCCCCCCCCCCCCCBCCCCCCDDDCCCCCCC
+@61DFRAAXX100204:1:102:8724:1888/1
+CGGGTGTGGTGCCAAGCATCCCTTGTTCTTGGAGNTATTGTATTCCTCTCTTTGGTTTCTTATTAAATAAATCAAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBB@B&28;88DCCCCCCCCCCCCCCDCCCCCBCCDC@BCA>@BD@B
+@61DFRAAXX100204:1:102:8903:16361/1
+CCTATAAGTTGTGCCAGCTCTAACTGACTGATGCNCTTCAGGATCTCATGCCACGAATTTCCTAAATAATTTCCAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:102:9691:18717/1
+ATAAGTTGTGCCAGCTCTAACTGACTGATGCACTNCAGGATCTCATGCCACGAATTTCCTAAATAATTTCCATCAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BABBACCCCCCC;CCCCCBCCCCCCCCCCCCCCCCDCCCAC
+@61DFRAAXX100204:1:103:10201:1449/1
+CTGAACACTAGAAAGGCATCCTTTTGTAAAATGTGGGAAAACTTAGCACCAGGTGAAGGTCCTGAAGAATTTCCAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCDCCCCCCCC?CCBCCCCCACC;CCCCCCC
+@61DFRAAXX100204:1:103:11572:6697/1
+CAAAATTGAAACTAAACATTCTAACCCCTTTTTTCGCAGGCTCAATTCCTGAACATTACTCATACCGAGTTCTTGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC8CDCCCCDD
+@61DFRAAXX100204:1:103:12517:20251/1
+GCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTCTGAAATGCAAGTTCTACTATGCTTTCAT
++
+CCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:103:13105:12342/1
+CTGGACTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATCCGGAAGAGAATGCGCAGCCCACACGCCAGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCBCCCB@CCCCCB?BCCCCCCB@C@B;
+@61DFRAAXX100204:1:103:13548:1359/1
+GGTGACTTTCGGATGTTAGAGTGAGGAAGAAGCTCAGCGCTTCCCTGCAGACGTTTAAAAGCCTCTGCTGGACTTC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCC+??AA?CCCCCCCCCCDCCDCBDCBCC@BBDDBDDDDBBABBACAAB
+@61DFRAAXX100204:1:103:13762:1440/1
+CTCCCTTCCCCCACCCCCAATTATAAACATTTTATCCTCCAAAATACAGCTCTCCTGAGTTGTACTTCTCGCTGAA
++
+CCCCCCCCCCCCCBBBBBBCCCCCCCCCC?CCCCCCCCCCCCACCCCCCCCCCCCCCCCDCCDCCCCCCCACCBB@
+@61DFRAAXX100204:1:103:13776:4298/1
+TGATATTTGAAATACTATTCCAATTCGCAGGAAAAATCTTCTAAGAACAGCACGCAGTTCCGGAATCAAGTCAAAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDC@BCC
+@61DFRAAXX100204:1:103:13798:6365/1
+GGTCACAGTCATAATTTACATAAATGTCCACCACACTCTGAGCATCTGCACAGATCCTTGTCAGTGTCTGAATAAC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCC
+@61DFRAAXX100204:1:103:14748:1375/1
+CCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGCCACCC
++
+CCCCCCCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCCCCCCCCCACCCDBD@@DDB
+@61DFRAAXX100204:1:103:16156:9928/1
+CATGAGCAATAATTTTTTTCTCCCTTCCCCCACCCCCAATTATAAACATTTTATCCTTCAAAATACAGCTCTCCTG
++
+CCCCCCCCCCCCCCCCCCBBBBCCCCCCCCCC@B@BB@CCCCCCCCCACCCCCCCCCCCCAACCCCCCCCCCCCCC
+@61DFRAAXX100204:1:103:16292:7311/1
+CTGGTTCTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDBCDCDCCCCCCCCCCBDC
+@61DFRAAXX100204:1:103:1757:15756/1
+GGCAAAAATATCATCCAAAAGTACATCGCTGAGAACTTCTAAATACTGGGTGAATACATCACATATTGCATAAAGG
++
+CCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:103:19512:1223/1
+CTGTTAAGCCCCTGGTTCTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCDCCDADBB@C@BB@
+@61DFRAAXX100204:1:103:2005:9846/1
+TGCTTCCCTGCAGACGTTTAAAAGCCTCTGCTGGACTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCBCCCCABDBBCBBDDDC
+@61DFRAAXX100204:1:103:2755:14644/1
+CTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCCACACCC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC=C
+@61DFRAAXX100204:1:103:3597:13520/1
+GTTGTTGTGATGTTAAAAAGCGGTACATTCCTTGGTCTTGAGTATCAACTCGAACATCGAAGTCTACTACATCTCT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCDCCCCCCCCCCCCCCCCCDCBCCCCDADDCDCDC
+@61DFRAAXX100204:1:103:4062:11566/1
+GATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCCACACCCTGTCTTCAGGTGCCACGCTCATG
++
+CCCCCCCCCCCCCBCCCCCCCCCCCCBCCCCC@CACCBCCCCCCCCCACCBCC=@BCBAC3;;-6AC@C@C?@:AB
+@61DFRAAXX100204:1:103:5147:16732/1
+CATGGTTACAAGTTGTTGTCATCCATTCAGCTTTCTCTGTCTGCTGTTCTGGCAATTTCATGTTGTCAAAGATTCT
++
+CCCCCCCCCC;????CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:103:6646:12936/1
+GTGCAACACATAGATACTGCTTGATAGCATTAATAAACATCTCATTTGTCCTGAAAACAGGTCCTGCATTCTGCAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCDC
+@61DFRAAXX100204:1:103:7220:15954/1
+GAGGAATTGTGGTTTTGAAGATATCCAGGGTGCAGTTACACGTTTTATCCCAGATTTCAAGAGTAAACTTTTCACC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCABCCCCCCCA
+@61DFRAAXX100204:1:103:7253:3680/1
+CTTTACATCTGTACCATATACATATCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:103:8055:11636/1
+TTCCTGATGATGATGTGGATTCTAAGGAGTTTAAACTTCCATATCTGTTTATAGTCTCTGGGTGTTTAACTTCACT
++
+CCCCCCCCCCCCCCCCCC<CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCBCDCCCABCCCDCC
+@61DFRAAXX100204:1:103:8348:14452/1
+GTCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTTTGTTATTTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDBCCDCCCDCCCBCB
+@61DFRAAXX100204:1:104:12460:3347/1
+CTGATGCTGTGGGAACAGCCTTTCTGCTCAACATGAGCCCAACACGAGACAGAGGCCACTGGGTTACTAAAGGGAC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCC@CCDCDDCCCCBCCDCBB@BBAAB
+@61DFRAAXX100204:1:104:12993:12947/1
+GGTGAATACATCACATATTGCATAAAGGACATGGTTACAAGTTGTTGTCATCCATTCAGCTTTCTCTGTCTGCTGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:104:13501:6860/1
+GTGATATTTGAAATACTATTCCAATTCGCAGGAAAAATCTTCTAAGAACAGCACGCAGTTCCGGAATCAAGTCAAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCBCCCCCCACCCDCBCC>A
diff -r 000000000000 -r b3fe7c4ca5aa test-data/reads.right.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.right.fq	Sat Mar 17 17:43:58 2018 -0400
@@ -0,0 +1,400 @@
+@61DFRAAXX100204:1:100:10494:3070/2
+CTCAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGC
++
+C<CCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCACCCCCACCC=
+@61DFRAAXX100204:1:100:10497:13422/2
+GAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCACCC
+@61DFRAAXX100204:1:100:10546:4478/2
+CTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCDCBCCCCCCCCCCCACCCCCCCCCBDC
+@61DFRAAXX100204:1:100:10609:6818/2
+AGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGCCCTTTATGCAATATGTGATGTATTCACCCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CBCC
+@61DFRAAXX100204:1:100:10648:5988/2
+AGATGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCACCCBCCBACC
+@61DFRAAXX100204:1:100:11486:13583/2
+CTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCBBBB@CCDCCCCDB@BDCCABCDDCBBCCCBC@
+@61DFRAAXX100204:1:100:1176:14271/2
+TGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCG
++
+CCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCDCCCCCCCCCC:BBBACCABC@CDDAB@DDCABDDABDBB
+@61DFRAAXX100204:1:100:12152:16425/2
+CCTTTCTAGTGTTCAGGTCATTGTGTAAGCTGTCAATGAAACCACTGTCAGATGGACCACCAGATCCAAAGTCTCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC=
+@61DFRAAXX100204:1:100:14680:13081/2
+CACAGCATCAGCCTACCTTTAGGGTCCTTCCCTGTCCTCTAAGCAGGGTGAGCCCACACTGTGGCAGGGACGGGAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCCCCCCCCCBCCDCCB'299@'9@
+@61DFRAAXX100204:1:100:16086:14019/2
+AGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTGAACATATAATGAAACGAAACAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCBCCCCCC
+@61DFRAAXX100204:1:100:17458:1622/2
+AAAACATTTGGGTTGAACTTTTAGTCTTTGGGGGAGTGGTGGTCATTTTGAGGGCTTGCTGTGCCCTGAATCTGTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@CCCCCBCCCCCCCDCCCDDCBDCBB@BABA=BBDB@AB<
+@61DFRAAXX100204:1:100:17716:21197/2
+GCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCAC?CCDBBCCBD@BCBBBB@B??BBA=@A?@
+@61DFRAAXX100204:1:100:19734:13092/2
+GGCTTTACTTACCGCAGTGACATCACAACACATAGAAATCCATGAAGGAACTGTGCTGCAAGCTGTGAGGACATGC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCC?CC@CBCCCBCAACCC
+@61DFRAAXX100204:1:100:2082:1789/2
+GGAGCAAGGATCAGTATGTGAACCCCAACTCTCAAACTACCCTTGGTCAGGAAAAACCCTCAGAGCAAGAGATACG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCBCBCCCBCDBBDACCDBCDCA@B##
+@61DFRAAXX100204:1:100:2172:8797/2
+TATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAA
++
+############################################################################
+@61DFRAAXX100204:1:100:2238:12815/2
+CCCCTCCAGACCCTTTAGAAACCCAGAGGCCTCGGGCTCGCGTGTGGCTCATTTTCGCCAGAAAGGCGGTTCCCAC
++
+############################################################################
+@61DFRAAXX100204:1:100:2327:5980/2
+CAAGACTGTGATGATACTGAAGTAGCCTCTCTTTGCCTAGAAGGGATAAGATGTGCTATCAGGATTGCATGCATTT
++
+CCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCACCCC?BCCCCACBCCBCCCCCCCDDDAA@CCDBBC
+@61DFRAAXX100204:1:100:3665:17139/2
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CCCCCC@CC@@CB@@@@DABBBCBBB
+@61DFRAAXX100204:1:100:6480:5393/2
+TGCTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCTACTCTTACTGAAATGCTGA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB
+@61DFRAAXX100204:1:100:8693:14085/2
+TGCAACCAAGGACAAACCCTTTTTGCTAGTGCAGATACTGCTTATGTTTTGGCCTACTCAATTATCATGTTGACTA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:100:9306:14527/2
+GCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCC
+@61DFRAAXX100204:1:100:9656:2687/2
+TAGAAATGGAACAGATGGCCAAGACGGCTAAAGCACTCATGGAAGCTGTGAGCCATGTTCAGGCACCTTTTACAAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCD3DBBCCCDCBBCCDCBDC
+@61DFRAAXX100204:1:101:11219:19264/2
+GTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@B@CBBCCCADDCCA@BC
+@61DFRAAXX100204:1:101:11349:8542/2
+GTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?DDD@CDDDDDBCBBCDDDBDABB)BBBB
+@61DFRAAXX100204:1:101:11674:10443/2
+CTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACG
++
+CCCCCCCCCCC@CCCCBC?CC@CBBCCC=C@CCCCAC:B@BBCC>@=@@@B>@BC@ACBB@>CBB=0;C@BBCC/?
+@61DFRAAXX100204:1:101:1179:19106/2
+AAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCBCCBBCCCCACCCCACCCCCCCCCCCCCCCCBABDB>D@BDDD@
+@61DFRAAXX100204:1:101:12110:12654/2
+GCAAGCACCACTGGTTTCTGTTTCTACTGTGAGTGAAGAAGTTAGCAAAGTGAAATCCACAGCAAAATTCCCAGAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCBCDCCCCCBCCCCCDCCBCDCCBCAACCDCCAA>BBC=B<B?B
+@61DFRAAXX100204:1:101:13165:4417/2
+GGACATTTATGTAAATTATGACTGTGACCTAAATGCAGCAAATATATTTGAAAGACTAGTAAATGACCTGTCGAAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAC
+@61DFRAAXX100204:1:101:13420:13159/2
+CCGGAAATCATCATCTTTCTGTGAAAATGTACAGAGATGCAGGTCTGTAATATAAAAATCTTAAACATATTGTTCC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCDCCCCCCCCC@@CCCCBCCCCCCDCDBC@
+@61DFRAAXX100204:1:101:14810:10441/2
+GGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCBCCCCCC
+@61DFRAAXX100204:1:101:15025:8342/2
+GCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCDCCDCDCACCB
+@61DFRAAXX100204:1:101:15551:15592/2
+GACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCCCCCCCDCC@
+@61DFRAAXX100204:1:101:16061:6897/2
+GGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCC
+@61DFRAAXX100204:1:101:16516:11581/2
+GATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTA
++
+C@CCCCCC@CCCCBBCBBCCC=@8@CC:CCCBC?C@@CC@C@>@@CCC>C>@>A<A8@8=<??<<=:C5>BCCBCC
+@61DFRAAXX100204:1:101:17825:1193/2
+AACGAAGCAGGTCTCCAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCCCCCCBCCCCCCACCCDC<ABBBA
+@61DFRAAXX100204:1:101:2920:3823/2
+CAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCA
++
+CCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCBCCCCCCCCCCCDCCCCCCCACCCCCCC=C?
+@61DFRAAXX100204:1:101:4549:18278/2
+GTCTGTAATATAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTA
++
+CCCCCCCCCACCCCC@@CCCBB?CCCCCCCCCCCCCCCCCCCCCCCCCCC@@@CC@=CC@@@C@@CCCCCCCCACC
+@61DFRAAXX100204:1:101:5059:19347/2
+AAGAAGACAATGTTGTCGATGGTCTGGATGAGTTCCAGCTGCACAACACATTTAATCAACAGGGCAGCAAACAATT
++
+CCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCDCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCBCDADCA?ACC
+@61DFRAAXX100204:1:101:5741:4886/2
+GGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTT
++
+CCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCACCCCBCC:CCCCCDCDCDCBCBCBC@BCCC@?BBCBCCBD
+@61DFRAAXX100204:1:101:6207:10801/2
+GGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
++
+CCCCCACCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCBCCCCACCCCCCCCD@BCBB@BBCABC
+@61DFRAAXX100204:1:101:6228:11229/2
+CTGTAATATAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAA
++
+CCBBCCCCCCCCC@@CCC>CCCBBC??>@BCCCCCBBCCCCC@CCCBC@@@CC@@CC@@@C@>CCCCCCCCCCC@C
+@61DFRAAXX100204:1:101:7284:17741/2
+AAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAATACCCATAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCB@CCBBBCBBCCCCCCCCCBCCCCCCCCCCBA
+@61DFRAAXX100204:1:101:7317:19738/2
+CATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCBCCCCCCAAC?BCCCCDCCCCCDC@
+@61DFRAAXX100204:1:101:7386:20759/2
+GATGTAGCCATATTTGCAGTAGACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCD@CACBDDB@CABCCCB@BBABBAABB>>BAB>?AA>AB
+@61DFRAAXX100204:1:101:7661:3279/2
+GCTGCAAGCTGTGAGGACATGCTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCD@CCC
+@61DFRAAXX100204:1:101:7989:14539/2
+TGACTACAGACCTTCACAGTCCACAGGTTAAAAACAAAATGACAAAAGAACAGTACATTAAAATGAATCGTGGTAT
++
+CDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBBBCCCCCCCC?BBCCCCCCCCCC@CCCCCCC?BCCBC=
+@61DFRAAXX100204:1:101:8630:9416/2
+GGCGCAGGCACCTCCACCGGCCCCGCCTTCTCTCCGCAAACGCTCCACGCACACAAAGGAGGCCCTTGAGCCTCAA
++
+############################################################################
+@61DFRAAXX100204:1:101:9622:17436/2
+ACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCACCBCCCBCCCCCCCC
+@61DFRAAXX100204:1:102:10071:12692/2
+GCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCAC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCDCCCCCDCCCCDCCCCCBC
+@61DFRAAXX100204:1:102:10556:11503/2
+CGGATCTGATATTTCCAGTGCAGAAAATGAACAGACAGAAGCTGATCAGGCAACTGCAGCTGAAACATTATCTAAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCDCCC
+@61DFRAAXX100204:1:102:10558:14342/2
+AGAGATGCAGGTCTGTAATATAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCBBCCBBBCBBC
+@61DFRAAXX100204:1:102:12109:19420/2
+AAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCBCCC@CCCCCCCC?CCBCCADCDCAB
+@61DFRAAXX100204:1:102:12757:13134/2
+CAACGGAGCAGATTGCGTCTCACACAGAGGAACGAGAGGAAGTCTGTAACGCTCAGAGACTTGATGACAGTTCTTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCBCCCDCCCCCBCDCDCDDDDDBDCBBBDCBDBDD
+@61DFRAAXX100204:1:102:13549:15464/2
+GCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCA
++
+CCCCCCCCCCCCCCCCCCBCDCCCCCCCCCBCCCCCCCCCCCCCBCCCACC@CCCCCCCBDCCC=CC?CC?CCACA
+@61DFRAAXX100204:1:102:13777:6235/2
+GAAGGCCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACACGACCATGAGCCGC
++
+############################################################################
+@61DFRAAXX100204:1:102:14960:18241/2
+GCTGCATTCAGTGTGGGTCTCCAAGACTGTGATGATACTGAAGTAGCCTCTCTTTGCCTAGAAGGGATAAGATGTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCACCCCCCCCCDC
+@61DFRAAXX100204:1:102:15063:6971/2
+GTATCTATCAGCCATTTATAACGAAATAGCTGGGAAAAAAATATCAATGAAAGAAACAAAAGAACTAACAATCCCT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBBCCCCCCCCCCCBBCC@BBCBBCCCCC?CCCAC
+@61DFRAAXX100204:1:102:16420:15231/2
+CTACTACCCTCTCTTATGTGAAATTATGCAATTTGACTTGATTCCGGAACTGCGTGCTGTTCTTAGAAGATTTTTC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCC@CCCCCCCC>@CCCCCCCCCBC@DCBCCC
+@61DFRAAXX100204:1:102:16908:12433/2
+TGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCDCCCCCBCCACCCCBCC
+@61DFRAAXX100204:1:102:17677:10400/2
+CAATCCCTACAAAGTCAACTAAACAGAATGTAGCCAGTGAAAAGCAAAGACGACTTCTGTATAACTTAGAAATGGA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCBCCCCACDCC;@BBB@C
+@61DFRAAXX100204:1:102:17711:7491/2
+TATAAACCAAGAGCATGAAGGGGATCTTGAGCCCCAAACACATGATGTGGATAAAAGTCTCCAAGATGATACAGAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCDCCCCCCCADC=DCCBCDA
+@61DFRAAXX100204:1:102:17798:2084/2
+AGTGAAGTTAAACACCCAGAGACTATAAACAGATATGGAAGTTTAAACTCCTTAGAATCCACATCATCATCAGGAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCDC
+@61DFRAAXX100204:1:102:18807:10059/2
+CTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCTACTCTTACTCAAATGCTGAAC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCACC
+@61DFRAAXX100204:1:102:19518:11565/2
+CTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCBCC@BCCCDBCCDABDDDDCDBCBDCBDDA
+@61DFRAAXX100204:1:102:2639:2051/2
+CAGGAGTCTATTGGAGAAACCAGCTCTCAAAGTGTGGTAGTTGCTGTGGATAGAATATTCACCGGATCCACAAGGC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCDCCACCDCCCCCACCBCB@<A88>>5?>@>@17>A1;5;:=;
+@61DFRAAXX100204:1:102:3101:2926/2
+GAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACC
++
+CCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCACCCCCCCCCCCDBCC
+@61DFRAAXX100204:1:102:5977:14503/2
+GAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCDCDCDCCCCCCDCDCCCCCDBCDCB
+@61DFRAAXX100204:1:102:6251:21399/2
+GTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCCCCDCCCCDCACCBCBCCBDDCC@D<BCBDDBDAB
+@61DFRAAXX100204:1:102:7093:4246/2
+GAAGATTTTTGCACACTCAGGCTATCTGAGACACCGGAAATCATCATCTTTCTGTGAAAATGTACAGAGATGCAGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCBCCBCB@ABBBADB@C=
+@61DFRAAXX100204:1:102:7907:21314/2
+GACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGACTTCT
++
+@@@9@#######################################################################
+@61DFRAAXX100204:1:102:8037:6949/2
+CTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAA
++
+CCCCCCCCCCCDCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCDCCCCCCCCADCBCCABCAD@C@
+@61DFRAAXX100204:1:102:8724:1888/2
+TGAACTCCTTAGAATCCACATCATCATCAGGAATTGGCAGCTACAGTACACAGATGTCTGGCACTGATAATCCAGA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@=B?@99;>?BB==<@=@A?B=<<BBB>DB2(?=;@
+@61DFRAAXX100204:1:102:8903:16361/2
+GCATTTTCAGCATTCAGCTGGAAAGAGATGCATATGTCCAAGCACTAGCCAGATTTACCTTACTTACAGTGAGTTC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCBCBCC
+@61DFRAAXX100204:1:102:9691:18717/2
+CTAGAAGGGATAAGATGTGCTATCAGGATTGCATGCATTTTCAGCATTCAGCTGGAAAGAGATGCATATGTCCAAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:103:10201:1449/2
+GAGACTATGAAGAAAAGCCACTTGATATTGTCCAGAGCATTGTAGAAGAAATGTTGAACATCATTGTTGGAGACAT
++
+CCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCBCCCCCCCDCBCCCCDCCCCCCCDCCCCDCA@BCBBB?
+@61DFRAAXX100204:1:103:11572:6697/2
+AGCTCATTTGACCATAAGTGGATGGTTATTCAGACACTGACAAGGATCTGTGCAGATGCTCAGAGTGTGGTGGACA
++
+CCCCCCCCCCCCCCCCCCAC???AAACCCCCCCCCCCCCCCCCCCBCCCCCCCC@CABCCCCAACBC>CB<A?:BB
+@61DFRAAXX100204:1:103:12517:20251/2
+CAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCCCDDCDCCCCCCCDCDDDBCD
+@61DFRAAXX100204:1:103:13105:12342/2
+TCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCBCDD@BAAA
+@61DFRAAXX100204:1:103:13548:1359/2
+GGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCBDCDCCCBDCCCBDDBCCDDCDCADDBDC@B
+@61DFRAAXX100204:1:103:13762:1440/2
+GAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCBCCCCCCCCDCCCDDCBCCCCB@BCC>
+@61DFRAAXX100204:1:103:13776:4298/2
+CCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCBCCCCCCCC
+@61DFRAAXX100204:1:103:13798:6365/2
+GTTTATTAATGCTATCAAGCAGTATCTATGTGTTGCACTCTCAAAAAACGGAGTCTCATCTGTTCCAGAGGTTTTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCDCCDDCDCCBDDC@
+@61DFRAAXX100204:1:103:14748:1375/2
+TAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAATACCCATA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@BCCB=CCBBBC@@CCCACCCACCCCBCCCDD>DC
+@61DFRAAXX100204:1:103:16156:9928/2
+CTCATGTTGAGCAGAAAGGCTGTTCCCACAGCATCAGCCTACCTTTAGGGTCCTTCCCTGTCCTCTAAGCAGGGTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCDCCCDCCDCCA@ACBABB?B
+@61DFRAAXX100204:1:103:16292:7311/2
+CACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAATTCACATGTAATGCAGCTTTCCCAGACACAAGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCC5CCCCDCCCCCBCCBCCCBDDDBDBBBBCD
+@61DFRAAXX100204:1:103:1757:15756/2
+TGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:103:19512:1223/2
+TGTCACTCTTGTATTTGAAAAACACTTTCCGGCCACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAA
++
+CCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC@CBA8=A=CCACCCBCCA#
+@61DFRAAXX100204:1:103:2005:9846/2
+TTTAATTCCAACAATGAACAGAGGGCTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
++
+CCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBDDBCDCCDBDCBCCDDDCDADBBDDC
+@61DFRAAXX100204:1:103:2755:14644/2
+GCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCACTCTTGTATTTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCACCCCC>CCC@CBACDCCDCC
+@61DFRAAXX100204:1:103:3597:13520/2
+CACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCACACDDCCDDCCB@A?B@BB@ABBBBADABD<?>AA
+@61DFRAAXX100204:1:103:4062:11566/2
+CAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATG
++
+CCCCCCCBCCCCCCCCCCCCC?CCCC=CCCCCA=@A@CCACBCC?ABAABCCCCACC>BC<CCCACCCCB@C@B@?
+@61DFRAAXX100204:1:103:5147:16732/2
+GGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCBCCCBCCCCCCCBCCBBCCBC
+@61DFRAAXX100204:1:103:6646:12936/2
+CTCCAATGATACTCAGGAATCTGGAAATTCTTCAGGACCTTCACCTGGTGCTAAGTTTTCCCACATTTTACAAAAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCC@CDCCDCCCCCDCCCDBDBADDC
+@61DFRAAXX100204:1:103:7220:15954/2
+GATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCCCCCCCCCCCCBCDC
+@61DFRAAXX100204:1:103:7253:3680/2
+GTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTT
++
+CCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@BCCCCCCCBCDCCCBCCCCCCB=CDA
+@61DFRAAXX100204:1:103:8055:11636/2
+AAATGACCTGTCGAAAATTGCACAAGGAAGGGGCAGCCAAGAACTTGGTATGAGTAATGTTCAGGAATTGAGCCTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCDCCCCDACCCCCCCCCACCCCC
+@61DFRAAXX100204:1:103:8348:14452/2
+AACATTTGGGTTGAACTTTTAGTCTTTGGGGGAGTGGTGGTCATTTTGAGGGCTTGCTGTGCCCTGAATCTGTTGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@CCCCCDCCCCCCCCCCCCCACBCCDCCCCCAB@CBCCDCBB
+@61DFRAAXX100204:1:104:12460:3347/2
+CACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCBCCC@@@BBCCCACBCCC@ACBC
+@61DFRAAXX100204:1:104:12993:12947/2
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTTGCCATTGTGCAAAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCC@CCACBCDDCBCC,BBC?BBBBB@BBBD
+@61DFRAAXX100204:1:104:13501:6860/2
+CTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCC
diff -r 000000000000 -r b3fe7c4ca5aa test-data/samples.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples.tsv	Sat Mar 17 17:43:58 2018 -0400
@@ -0,0 +1,4 @@
+ConditionA	CondA_replicate1
+ConditionA	CondA_replicate2
+ConditionB	CondB_replicate1
+ConditionB	CondB_replicate2
diff -r 000000000000 -r b3fe7c4ca5aa trinity.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinity.xml	Sat Mar 17 17:43:58 2018 -0400
@@ -0,0 +1,295 @@
+<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.3">
+    <description>de novo assembly of RNA-Seq data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive"><![CDATA[
+        if [ -z "\$GALAXY_MEMORY_MB" ] ; then
+            GALAXY_MEMORY_GB=1 ;
+        else
+            GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ;
+        fi ;
+
+        if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
+            workdir=`pwd` ;
+            cd "\$TRINITY_SCRATCH_DIR" ;
+        fi ;
+
+        #if $additional_params.guided.is_guided == "yes":
+            ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' &&
+            ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' &&
+        #end if
+        Trinity --no_version_check
+
+        ## Inputs
+        #if $pool.pool_mode == "Yes":
+            #if str($pool.inputs.paired_or_single) == "single":
+                --single ${ ','.join(['"%s"' % x for x in $pool.inputs.input]) }
+                #if $pool.inputs.input[0].is_of_type('fasta'):
+                    --seqType fa
+                #else:
+                    --seqType fq
+                #end if
+    
+                #if $pool.inputs.strand.is_strand_specific:
+                    --SS_lib_type $pool.inputs.strand.library_type
+                #end if
+            #elif str($pool.inputs.paired_or_single) == "paired":
+                --left ${ ','.join(['"%s"' % x for x in $pool.inputs.left_input]) }
+    
+                --right ${ ','.join(['"%s"' % x for x in $pool.inputs.right_input]) }
+    
+                #if $pool.inputs.left_input[0].is_of_type('fasta'):
+                    --seqType fa
+                #else:
+                    --seqType fq
+                #end if
+                @COMMAND_PAIRED_STRAND_JACCARD@
+            #elif str($pool.inputs.paired_or_single) == "paired_collection":
+                --left ${ ','.join(['"%s"' % x.forward for x in $pool.inputs.pair_input]) }
+                --right ${ ','.join(['"%s"' % x.reverse for x in $pool.inputs.pair_input]) }
+                #if $pool.inputs.pair_input[0].forward.is_of_type('fasta'):
+                    --seqType fa
+                #else:
+                    --seqType fq
+                #end if
+                @COMMAND_PAIRED_STRAND_JACCARD@
+            #end if
+        #elif $pool.pool_mode == "No":
+            #if $pool.inputs.paired_or_single == "unmerged_paired_collection":
+                --left $pool.inputs.pair_input.forward
+                
+                --right $pool.inputs.pair_input.reverse
+    
+                #if $pool.inputs.pair_input.forward.is_of_type('fasta'):
+                    --seqType fa
+                #else:
+                    --seqType fq
+                #end if
+                @COMMAND_PAIRED_STRAND_JACCARD@
+            #elif $pool.inputs.paired_or_single == "unmerged_single_collection":
+                --single $pool.inputs.input
+    
+                #if  $pool.inputs.input.is_of_type('fasta'):
+                    --seqType fa
+                #else:
+                    --seqType fq
+                #end if
+    
+                #if $pool.inputs.strand.is_strand_specific:
+                    --SS_lib_type $pool.inputs.strand.library_type
+                #end if
+            #end if
+        #end if
+        $norm
+
+        ## Additional parameters.
+        #if $additional_params.min_contig_length:
+            --min_contig_length $additional_params.min_contig_length
+        #end if
+        #if $additional_params.long_reads:
+            --long_reads $additional_params.long_reads
+        #end if
+        #if $additional_params.guided.is_guided == "yes":
+            --genome_guided_bam 'localbam.bam'
+
+            #if $additional_params.guided.genome_guided_min_coverage:
+                --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage
+            #end if
+
+            #if $additional_params.guided.genome_guided_min_reads_per_partition:
+                --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
+            #end if
+
+            #if $additional_params.guided.genome_guided_max_intron:
+                --genome_guided_max_intron $additional_params.guided.genome_guided_max_intron
+            #end if
+        #end if
+
+        #if $additional_params.min_kmer_cov:
+            --min_kmer_cov $additional_params.min_kmer_cov
+        #end if
+
+        ## CPU and butterfly options.
+        --CPU \${GALAXY_SLOTS:-4} --max_memory \${GALAXY_MEMORY_GB:-1}G --bflyHeapSpaceMax \${GALAXY_MEMORY_GB:-1}G --bfly_opts '-V 10 --stderr'
+
+        ## > $trinity_log 2>&1
+
+        &&
+
+        if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
+            mkdir -p "\$workdir/trinity_out_dir";
+            cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir";
+            cd "\$workdir";
+        fi ;
+
+    ]]></command>
+    <inputs>
+        <conditional name="pool">
+            <param name="pool_mode" type="select" label="Are you pooling sequence datasets?" help="" >
+                <option value="No">No</option>
+                <option value="Yes" selected="True">Yes</option>
+            </param>
+            <when value="Yes" >
+                <conditional name="inputs">
+                    <param name="paired_or_single" type="select" label="Paired or Single-end data?">
+                        <option value="single" selected="true">Single-end</option>
+                        <option value="paired">Paired-end</option>
+                        <option value="paired_collection">Paired-end collection</option>
+                    </param>
+                    <when value="single">
+                        <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/>
+                        <conditional name="strand">
+                            <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
+                            <when value="false">
+                            </when>
+                            <when value="true">
+                                <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
+                                    <option value="F">F</option>
+                                    <option value="R">R</option>
+                                </param>
+                            </when>
+                        </conditional>
+                    </when>
+                    <when value="paired">
+                        <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger" multiple="true" label="Left/Forward strand reads" />
+                        <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger" multiple="true" label="Right/Reverse strand reads" />
+                        <expand macro="input_paired_strand_jaccard" />
+                    </when>
+                    <when value="paired_collection">
+                        <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/>
+                        <expand macro="input_paired_strand_jaccard" />
+                    </when>
+                </conditional>
+            </when>
+            <when value="No">
+                <conditional name="inputs">
+                    <param name="paired_or_single" type="select" label="Paired or Single-end data?">
+                        <option value="unmerged_single_collection">Single-end</option>
+                        <option value="unmerged_paired_collection">Paired-end</option>
+                    </param>
+                    <when value="unmerged_single_collection">
+                        <param name="input" argument="--single" type="data" format="fasta,fastqsanger" label="Single-end reads" help="Elements of collection will NOT be merged"/>
+                        <conditional name="strand">
+                            <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
+                            <when value="false">
+                            </when>
+                            <when value="true">
+                                <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
+                                    <option value="F">F</option>
+                                    <option value="R">R</option>
+                                </param>
+                            </when>
+                        </conditional>
+                    </when>
+                    <when value="unmerged_paired_collection">
+                        <param name="pair_input" type="data_collection" collection_type="paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Pair dataset collection. The paired datasets will NOT be merged"/>
+                        <expand macro="input_paired_strand_jaccard" />
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+        <param name="norm" type="boolean" argument="--normalize_reads" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
+        <section name="additional_params" title="Additional Options" expanded="False">
+            <param name="min_contig_length" argument="--min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
+
+            <conditional name="guided">
+                <param name="is_guided" type="select" label="Use the genome guided mode?" help="If you already mapped the reads to the genome, Trinity can use this information">
+                    <option value="no">No</option>
+                    <option value="yes">Yes</option>
+                 </param>
+                <when value="no">
+                </when>
+                <when value="yes">
+                    <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
+                    <param name="genome_guided_max_intron" argument="--genome_guided_max_intron" type="integer" value="" min="1" label="Maximum allowed intron length (also maximum fragment span on genome)"/>
+                    <param name="genome_guided_min_coverage" argument="--genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
+                    <param name="genome_guided_min_reads_per_partition" argument="--genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
+                </when>
+            </conditional>
+
+            <param name="long_reads" argument="--long_reads" type="data" format="fasta" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
+
+            <param name="min_kmer_cov" argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="pool_mode" value="No" />
+            <param name="paired_or_single" value="unmerged_paired_collection"/>
+            <param name="pair_input">
+                <collection type="paired">
+                            <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
+                            <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
+                </collection>
+            </param>
+            <param name="is_strand_specific" value="true"/>
+            <param name="norm" value="true"/>
+            <param name="library_type" value="RF"/>
+            <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" />
+        </test>
+        <test>
+            <param name="pool_mode" value="No" />
+            <param name="paired_or_single" value="unmerged_single_collection"/>
+            <param name="input" value="reads.left.fq" ftype="fastqsanger"/>
+            <param name="is_strand_specific" value="true"/>
+            <param name="norm" value="false"/>
+            <param name="library_type" value="F"/>
+            <output name="assembled_transcripts" file="raw/Trinity_single_unmerged_1.fasta" compare="sim_size" delta="500" />
+        </test>
+        <test>
+            <param name="pool_mode" value="Yes" />
+            <param name="paired_or_single" value="paired"/>
+            <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
+            <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
+            <param name="is_strand_specific" value="true"/>
+            <param name="norm" value="false"/>
+            <param name="library_type" value="RF"/>
+            <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
+        </test>
+        <test>
+            <param name="pool_mode" value="Yes" />
+            <param name="paired_or_single" value="paired"/>
+            <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
+            <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
+            <param name="is_strand_specific" value="true"/>
+            <param name="norm" value="true"/>
+            <param name="library_type" value="RF"/>
+            <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
+        </test>
+        <test>
+            <param name="pool_mode" value="Yes" />
+            <param name="paired_or_single" value="paired_collection"/>
+            <param name="pair_input">
+                <collection type="list:paired">
+                    <element name="pair1">
+                        <collection type="paired">
+                            <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
+                            <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
+                        </collection>
+                    </element>
+                    <element name="pair2">
+                        <collection type="paired">
+                            <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
+                            <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
+                        </collection>
+                    </element>
+                </collection>
+            </param>
+            <param name="is_strand_specific" value="true"/>
+            <param name="norm" value="true"/>
+            <param name="library_type" value="RF"/>
+            <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
+        </test>
+    </tests>
+    <help>
+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+
+.. _Trinity: http://trinityrnaseq.github.io
+    </help>
+    <expand macro="citation" />
+</tool>