Mercurial > repos > pjbriggs > trimmomatic
changeset 11:59054f086eca draft
Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
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--- a/README.rst Mon Mar 05 10:13:48 2018 -0500 +++ b/README.rst Fri Oct 05 05:19:17 2018 -0400 @@ -71,6 +71,8 @@ ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- +0.36.6 - Added trimlog and log outputs; add support for ``fastqillumina`` + and ``fastqsolexa`` input types 0.36.5 - Remove tool_dependencies.xml and always use conda to resolve tool dependencies 0.36.4 - Add option to provide custom adapter sequences for ILLUMINACLIP @@ -110,10 +112,10 @@ ======= This wrapper has been developed and is maintained by Peter Briggs (@pjbriggs). -Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed +Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed support for gz compressed FastQ files. Charles Girardot (@cgirardot) and Jelle Scholtalbers (@scholtalbers) contributed additional options to ILLUMINACLIP. - +Matthias Bernt (@bernt-matthias) added log and trimlog output. Developers ==========
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Illumina_SG_R1.fastqillumina Fri Oct 05 05:19:17 2018 -0400 @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNTCATAACCGTAAAGGCCAGAGACGAGAACCACTCGCAGGCAAGGTTTGCAAGCCTCGCCAAGAATATTATAGACCCGCTTGCCAACGACTGGCATTACATCACCGTAAAGAAGGTAGGCAAGAATCACTGGATCAGCATAACAGATGAGGGTAGAGACGCCGTATCGTTTCTGGGCTAGGTTATCTGGGCCGCCTTCTTGCGTCGGCGCACAGTCACAAAGGAAATGCC ++ +^^^^^aaa_aaaa^aaeeeeBUUd`egggbdedcefgggge_ceg`bdde_eceggggdddggge^efdgegcdefggbdgdeggggeeebeceeeeaddddddddddda^dddddddddddaadd^bd^Y`bbbI^^b``ddbdY^db`Y^`I^dddd^dddd^O``bN^WHOOIIOYWFWZSWI^WNW^`ddddWY`IWIOYIIOIIY^b^SWO^dd^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNAGAGTCCGATTACTTTAGAACAGTGCCGCGAATCCTTCGTCAACTGTAATCCAAGCGACATTGGTTCGATTAGCACGCATGAGGCACGAGATCTACGCGTATCTCTGGTAGATACACCAGGAGGGATGAGAGTTGAGCGAGTTAGCTGTGGCCAGAGAGATGGGTCTAATCGTAGTCTACAACTGGGAGTCACATGCCACTACCGACTAATCTGGTCGCCGAACGGGAG ++ +^^^^^aaacccc`cccd_eeBUUbebeggadgghhhghhggeggfgggggggggghghgheggggggdfeghgghhhggggggggbegggggggeeeeeeddddeededdaadddeed_dWZddeeedeIY`dddddeeed``d`^`^`b`de^bddedcQ[M^``dbd`dedddW^^`W^b``dP^ddd^`dIWWW`ddddeddee`W`W^`bd`ddd`d^bY^^dcQ[dYbIY^IYW^dc[]WMHW^[ +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGGTTACCACTATACTCCCGTTTCTATATTCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGGTTGCCGTCTTCTGCTTGAAAAAAAAAAACAAACAAGAGAAGACGACGTACTGCACCACCA ++ +^[K[^aaaaaaaaaaaeeeeBU`bdbbdbVWbd\bfgdgVbgbgefg`cfgggbbbggd[cegeeeeceeeeeecececcdddddddddb`ddddZ^adddaddabdZbZSWZH^``bbddd^``^Y^dWW`ddYbd^``ddddY^IIIOYI^^``dddddd`^MWZdBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGGGCTCAGCGCTNTGCAAATTCTAGTTAGAAACTCACAGTTCTGACAAGCCTTAGGTCAGTGTGATTGGCGGTTAGTCAACTCGGAGAAAGCGTCTTTTCCCGACTTGAATGGTTTGTCCCGACAGTTCGTTGACTGGGGTTTCGTCAGCCTTGAGCGGGGTTCCATCCATCTTTATCGCGCCTTGGGAAAGTAGTCGGCGGGCTTCGGGGTTGGGTGAGGGCAATCCTTGTTCGGTCAAAA ++ +T\\\\]N[______]_bbbdBUU]`bddddfffffffeeedeceeeee\bcdeeeedcdeeeeeb\`daeL``_bdZdbcT[T[\\b\\cdddHWRbc\\_JS_cddI[cP[HP_ZWWWIXOZIPXWW_HQHFSZ\ddBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGGGTCACAGGGTCAGACTGGGTGACCTTCATGAAGCGTCTGGTGACGTAGCTGTGATAGTCCAGCTTGGCAACCTCTGCTGGTTGCAGAGG ++ +^^K[^aaaccccccc[eee_ebZeeeadegggbccggfgggcfgggeggd`^dd`ddgcdegggggedbegggegcgddggbegVbdegcdggbeggegge\eeececeeeeddddccdeddd[aabdabdK\\`dPYY``ddbddI^I``dee^^]c^HWHY`W^db^WIIIOIOOYW^IHOIPY^b`bbY``^ZH^dde`ddbdWWIHP`IPOIPYIP^Y`bYY`HIYYIW`bddd^BBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA ++ +^^^^^aaaccccccccffffffhhhggeeggggggggggdggdggggghhgggggedghhhgghgghghghhhhhggggggggggggggggcggggggggfdcefffffffZbdfdfbdfffffW]ffffdffddbdffffcWdcff`dfddffbdYbffWbddff^^^bdd[cfWbbI^^]cfMW[`ffffbddfIbQ[fbbdbdIY^bd^bdXbYbYbY^bIPIIOPOYI^dWQFQ[fbdBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC +GTAGTATTCTCATATCACAAGTCCCCAAACTGCATAAGGTGTGGAGTGGAGTGTCTCCCACTGCATTTTGTTGGTTTGGGTTGCATTTTTTGTGGCACAAAATTATCTTTAAACACTCTAAGCTCATATTTGCACATGCAACATGAATTGGAGCATTTCTTTTGCAGTCAACTGCCAGTACATTAACTCCACTCTGTAATAGTAAATCCTGTCTCTTATCCACATCTCCGAGCCCACGAGAATAAGGCGA ++ +TTKKT^Xaaaaa[[aaeeeeeeeggeadegegggecebeO`X_]XcXcefZeggggfggeeeeggggdbcbdee]dedddd_bcedeggfggggdgcfggegcegeggggeeggg_ecc^^ceeeecaaddadddddddddddddddddKZ^bdbZbddddba^bddddddddbddd^b^bdIO^IIINYYY^YIN^Y`YYIINYIY`bd^OYYY`YYIIIOOYYIN^bWWW^^dddBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGGCCAGCCAAACCTGT ++ +^^^^^aaacacccccceeeeeeghghgggggghgheffgegggghheghgg^ddfggggggLdfdggbdggggg_eceedeeT_dddeededZ`dbbdZ`ddddd`^W^`dccddceecdQ]]ddee[[[Q]c^cdddIYb^``[]W`debddY^b^ddd^bdeddO^Yd^`bddbcW]dd]HW]dYbddddddcMH^`d^^`^Y`^I^^YbO^bbd^```YWWMWW^YYbYb^IWHS`^`BBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCATGAGGTAGCAGACCAGTGCCAGAGATAGTGACCACAGTGTTGGCCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAGACTTTTAAAAAACCGATCTACACCTTGACAGGCTATTAAAGGAAACTGGCCTGGTATCACAG ++ +\T\\\[]JT[T[JT\_bbZWbdddddZLW`becdMVbWVbeL`]d]d\eedII]]T`dc`ddcLTLT``cb\cJ\ccd[JJRJbbcXcbcJ\_RYcddddcc[_cIXcdXXZ_Z_dd_Z__dddV__W_Y___ZXddFSSX^[[dZ\d[[ZWGUZ^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC +TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAGGCCATCCTCGGCCTGTCAGCCTGCCCCTCCCTCCCTCACCAGCTAGCCTCCTATGCCGCGGTAGGGGGCTCAAAGAGATTCAGACACAGCCACGTAATCATGTTACTTGCCCATTCCCCCCTCCCTCCTCCTCCTCTCCCCCCCTCTCTTCCCCTCTCCCCTCCCCTCCTCCCCTCCTGTCCCTTATACACATC ++ +\KK[\]]]_____X__bbdd_ddJJJUbWLJJbdbdJ]cbb]__deeeedddcddTTJ`bdeZLbJ]ddJJba`LLT`JJbcbJS[[J\cd\bcdd_J_XcYcJSZ_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Illumina_SG_R1.fastqsolexa Fri Oct 05 05:19:17 2018 -0400 @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNTCATAACCGTAAAGGCCAGAGACGAGAACCACTCGCAGGCAAGGTTTGCAAGCCTCGCCAAGAATATTATAGACCCGCTTGCCAACGACTGGCATTACATCACCGTAAAGAAGGTAGGCAAGAATCACTGGATCAGCATAACAGATGAGGGTAGAGACGCCGTATCGTTTCTGGGCTAGGTTATCTGGGCCGCCTTCTTGCGTCGGCGCACAGTCACAAAGGAAATGCC ++ +^^^^^aaa_aaaa^aaeeee>UUd`egggbdedcefgggge_ceg`bdde_eceggggdddggge^efdgegcdefggbdgdeggggeeebeceeeeaddddddddddda^dddddddddddaadd^bd^Y`bbbH^^b``ddbdY^db`Y^`H^dddd^dddd^O``bN^WGOOHHOYWEWZSWH^WNW^`ddddWY`HWHOYHHOHHY^b^SWO^dd^`>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNAGAGTCCGATTACTTTAGAACAGTGCCGCGAATCCTTCGTCAACTGTAATCCAAGCGACATTGGTTCGATTAGCACGCATGAGGCACGAGATCTACGCGTATCTCTGGTAGATACACCAGGAGGGATGAGAGTTGAGCGAGTTAGCTGTGGCCAGAGAGATGGGTCTAATCGTAGTCTACAACTGGGAGTCACATGCCACTACCGACTAATCTGGTCGCCGAACGGGAG ++ +^^^^^aaacccc`cccd_ee>UUbebeggadgghhhghhggeggfgggggggggghghgheggggggdfeghgghhhggggggggbegggggggeeeeeeddddeededdaadddeed_dWZddeeedeHY`dddddeeed``d`^`^`b`de^bddedcQ[M^``dbd`dedddW^^`W^b``dP^ddd^`dHWWW`ddddeddee`W`W^`bd`ddd`d^bY^^dcQ[dYbHY^HYW^dc[]WMGW^[ +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGGTTACCACTATACTCCCGTTTCTATATTCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGGTTGCCGTCTTCTGCTTGAAAAAAAAAAACAAACAAGAGAAGACGACGTACTGCACCACCA ++ +^[K[^aaaaaaaaaaaeeee>U`bdbbdbVWbd\bfgdgVbgbgefg`cfgggbbbggd[cegeeeeceeeeeecececcdddddddddb`ddddZ^adddaddabdZbZSWZG^``bbddd^``^Y^dWW`ddYbd^``ddddY^HHHOYH^^``dddddd`^MWZd>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGGGCTCAGCGCTNTGCAAATTCTAGTTAGAAACTCACAGTTCTGACAAGCCTTAGGTCAGTGTGATTGGCGGTTAGTCAACTCGGAGAAAGCGTCTTTTCCCGACTTGAATGGTTTGTCCCGACAGTTCGTTGACTGGGGTTTCGTCAGCCTTGAGCGGGGTTCCATCCATCTTTATCGCGCCTTGGGAAAGTAGTCGGCGGGCTTCGGGGTTGGGTGAGGGCAATCCTTGTTCGGTCAAAA ++ +T\\\\]N[______]_bbbd>UU]`bddddfffffffeeedeceeeee\bcdeeeedcdeeeeeb\`daeL``_bdZdbcT[T[\\b\\cdddGWRbc\\_JS_cddH[cP[GP_ZWWWHXOZHPXWW_GQGESZ\dd>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGGGTCACAGGGTCAGACTGGGTGACCTTCATGAAGCGTCTGGTGACGTAGCTGTGATAGTCCAGCTTGGCAACCTCTGCTGGTTGCAGAGG ++ +^^K[^aaaccccccc[eee_ebZeeeadegggbccggfgggcfgggeggd`^dd`ddgcdegggggedbegggegcgddggbegVbdegcdggbeggegge\eeececeeeeddddccdeddd[aabdabdK\\`dPYY``ddbddH^H``dee^^]c^GWGY`W^db^WHHHOHOOYW^HGOHPY^b`bbY``^ZG^dde`ddbdWWHGP`HPOHPYHP^Y`bYY`GHYYHW`bddd^>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA ++ +^^^^^aaaccccccccffffffhhhggeeggggggggggdggdggggghhgggggedghhhgghgghghghhhhhggggggggggggggggcggggggggfdcefffffffZbdfdfbdfffffW]ffffdffddbdffffcWdcff`dfddffbdYbffWbddff^^^bdd[cfWbbH^^]cfMW[`ffffbddfHbQ[fbbdbdHY^bd^bdXbYbYbY^bHPHHOPOYH^dWQEQ[fbd>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC +GTAGTATTCTCATATCACAAGTCCCCAAACTGCATAAGGTGTGGAGTGGAGTGTCTCCCACTGCATTTTGTTGGTTTGGGTTGCATTTTTTGTGGCACAAAATTATCTTTAAACACTCTAAGCTCATATTTGCACATGCAACATGAATTGGAGCATTTCTTTTGCAGTCAACTGCCAGTACATTAACTCCACTCTGTAATAGTAAATCCTGTCTCTTATCCACATCTCCGAGCCCACGAGAATAAGGCGA ++ +TTKKT^Xaaaaa[[aaeeeeeeeggeadegegggecebeO`X_]XcXcefZeggggfggeeeeggggdbcbdee]dedddd_bcedeggfggggdgcfggegcegeggggeeggg_ecc^^ceeeecaaddadddddddddddddddddKZ^bdbZbddddba^bddddddddbddd^b^bdHO^HHHNYYY^YHN^Y`YYHHNYHY`bd^OYYY`YYHHHOOYYHN^bWWW^^ddd>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGGCCAGCCAAACCTGT ++ +^^^^^aaacacccccceeeeeeghghgggggghgheffgegggghheghgg^ddfggggggLdfdggbdggggg_eceedeeT_dddeededZ`dbbdZ`ddddd`^W^`dccddceecdQ]]ddee[[[Q]c^cdddHYb^``[]W`debddY^b^ddd^bdeddO^Yd^`bddbcW]dd]GW]dYbddddddcMG^`d^^`^Y`^H^^YbO^bbd^```YWWMWW^YYbYb^HWGS`^`>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCATGAGGTAGCAGACCAGTGCCAGAGATAGTGACCACAGTGTTGGCCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAGACTTTTAAAAAACCGATCTACACCTTGACAGGCTATTAAAGGAAACTGGCCTGGTATCACAG ++ +\T\\\[]JT[T[JT\_bbZWbdddddZLW`becdMVbWVbeL`]d]d\eedHH]]T`dc`ddcLTLT``cb\cJ\ccd[JJRJbbcXcbcJ\_RYcddddcc[_cHXcdXXZ_Z_dd_Z__dddV__W_Y___ZXddESSX^[[dZ\d[[ZWFUZ^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC +TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAGGCCATCCTCGGCCTGTCAGCCTGCCCCTCCCTCCCTCACCAGCTAGCCTCCTATGCCGCGGTAGGGGGCTCAAAGAGATTCAGACACAGCCACGTAATCATGTTACTTGCCCATTCCCCCCTCCCTCCTCCTCCTCTCCCCCCCTCTCTTCCCCTCTCCCCTCCCCTCCTCCCCTCCTGTCCCTTATACACATC ++ +\KK[\]]]_____X__bbdd_ddJJJUbWLJJbdbdJ]cbb]__deeeedddcddTTJ`bdeZLbJ]ddJJba`LLT`JJbcbJS[[J\cd\bcdd_J_XcYcJSZ_>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Illumina_SG_R2.fastqillumina Fri Oct 05 05:19:17 2018 -0400 @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC +GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAGCGGGTCTATAATATTCTTGGCGAGGCTTGCAAACCTGGCCTGCGAGTGGT ++ +^^`^^`aacccccccceedddeghhhhgghhgheghhgggegghhhhhgggegghhhhhheeegghhgfcdgg``dggggeggggc\daadddddeeeeddddbdeeddeeeWI^^``^Z]cdddeeeeI^W`dbedeeeeeed`dddbeeebdddeeeeeedded`bddb^b``bdeddded^O^d`b```dd``bdd`IMSWMFOIPYY`^b``^bbYYSFFSFOOFWY^`W^dBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC +GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATGTGACTCCCCGTTGTAGACTACGATTAGACCCATCTCTCTGGCCACAGCTAACTCGCTCAACTCTCATCCCTCCTGGGGTATCTACCAGCGATACGCGTAGAACTCGTGCCTCATGC ++ +^^^^^aaaccccccccfeefffgggghggggggghgggghgabddgeeggghhgeggghhhhhhhgheafefegggghgd_dddggeeggee^begggggfffffffffffffffffffdbfffZddYbdfff^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAGNNCGCCGCTAAGACTGCCGTCAAATTCCTGAGCGGTAGTGATGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCGGGGGGCGCCGGCACATTCAAAAAAAAAAAACAGGAAAATGACATAGGCGTGTGTGA ++ +^^```aaacccccdccffbeffggheegggBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBUU^\BBSUU__dddfbffb]bd[dfddfdfbdfdffffWW[^P^b^dfbd^ddb^bb^bbdffbffbfbW^bb`b[``FQQQW]IOIPbY^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCCGCCTACTTTCCCAAGGCGCGATAAAGATTGATGGAACCCCGCCCAAGGCTGACGAAATCCCCGCCAACGAACTGTCGGGCCGACCCATTCAAGTGGGGAAAAAAACCTTTCCCCGGGTTGACAAACCGCCAAACAACCTCACCAA ++ +^^^^Xa^^^`cX^accddccccgggggegegeegggggggggdgg]bdfggefggfgg\eggggbJbfdabb[be_KSbe_beaeeeece^aSac__cH]bdUaaHHMHMY```dd^`^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGAGCCTCTGCAACCAGCAGAGGTTGCCAAGCTGGACTATCACAGCTACGTCACCAGACGCTTCATGAAGGTCACCCAGTCTGACCCTGTGAACCAGGCCGGG ++ +`^^`^aaaccccccccffffffgdeggfdggghgdgggggcgadgfeeedffcddcfffffdffddbd^dfbdfdfffbdddffbddffScZZS`ffffffW]ff`^dfffddfddfffbffdfdffffcW[``cdbdbdff^bbbYWbbFFWYbY^bbdI^HObbOYI^YbY^bbbW^bbdbXIYYbbbb^bIYYMbdffdbXXbSFHHMOOIYbY^IPOYbbBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC +GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATTGAGAATCCGCTAGCGGATAAGATTTTGCGGGGGGAGTTGGCGGAGGGCGATCGCTTGATGCTTGATTATGGAGGGGAGGGGGAGAAGATAGGTTTTACGAAAATAGAGGCGGAGGGGTCGGCGGCATAGAGGGTAATTTTTTGGGTTTTTTTCTGTGTCTTATACACAACTGAACGTGCCGACGAGCGG ++ +^^^^^_^accccccccedddeeghhgdggggcgggggdggggggW`ceeeceecPcZ]PKZZZZRaKRaZZIYaZPZFFOYYOIPY`IYZ]ccFSFWMYY``]cQQ]c`]FFOMMOW^IY`IP^YIO^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGAACAAG ++ +^^^^^aaaccccccccfbefefhhhhhgeghhhhghgef\dgghfhhhheghgcfgfggghghg\bfgffgegggegefggegN`bceff^ed^bceeggggghhgeggh]bdcfeggggggggceggegggee`eeffffffdcdf]]c`bbZ^dff]bdd`]`d`bbdd^YbYYbbYYYbYbd[b[XbY^b^I^bddbbbIYb^b^dY^YbYbYbbbbdY^bPIOIPPMWbHQ^FSW]fBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC +GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCGTCCTGGTTTGCGTCGGGGATGCGGTCACCCTCTAAAAGATTTATGGAGGTCGTCTCTTGTGTCTGGGCCGGGGGGAAGATGT ++ +^^^^^aaaccccccccffffffhhghheggghgghegfgffgghghhcdeegde_ceghhghhhfg`bcbeeggghghhghgfgggafefddggggegeeggcecbdffeffefff_caddddfb]bddffffffdO^bcfffc]ddQbdWbdfdd[]]]HYbddfc`FSQWbdY^XbbSWQW]FS[HOY]FOSHP^dIWYPbb^^HYbbddbbIIWHOTSW^bIY^YIOPOIYbbBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC +GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCCGTGGGCGCCGCATCATTAAAAAAAAAAAAAAAAAACATAACTCTCAAACGCGAATAGAGCAAGAAACAGACAGCTAAAGTACAAACAAT ++ +TT[^^^^^cccaaccaeeeeeebgghhgghhhhhhhgfgghhhhggfghhgegghhhhgggbcghhhgeeghhhhhbeeghgdbfbfdghg\eggggggggggeZeeeeecceeeeeeedeeeededace`dd`dd_ddcc]cccWWOY^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAGAGGAGGAGGAGAGAAGGGGGAATGAGCAAGTAACATAATTACATAGCTGTGTCTGAATCTCTTTGAGCACCCTACCTCGGCATAGGAGGCTAGCTGGTGAGGGAGGGAGGGGCAGACTGACAGGCCGAGGATGGCCTTGTGGTTGGCAAACTCCGTGGGGCGAGTCTGGGCTGCTGCATGCGCATCTGAGACTGGCTCTTGTACACATC ++ +^^^^^_X_a^a^aaaadddea__ddgdb^aeLbd_ccdgKTJTbK]_JbdJ[^\dLbedbdggcacK^ceeKScccaeZ\aZZaacZcKaS\adddddbaKKaaZ^b^bddddIZZbY`b^bZ^bbY`ddd^dW`bdYOY`^``W`SM^^W^WQSWHWY`bddd^dHSZ^Z^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Illumina_SG_R2.fastqsolexa Fri Oct 05 05:19:17 2018 -0400 @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC +GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAGCGGGTCTATAATATTCTTGGCGAGGCTTGCAAACCTGGCCTGCGAGTGGT ++ +^^`^^`aacccccccceedddeghhhhgghhgheghhgggegghhhhhgggegghhhhhheeegghhgfcdgg``dggggeggggc\daadddddeeeeddddbdeeddeeeWH^^``^Z]cdddeeeeH^W`dbedeeeeeed`dddbeeebdddeeeeeedded`bddb^b``bdeddded^O^d`b```dd``bdd`HMSWMEOHPYY`^b``^bbYYSEESEOOEWY^`W^d>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC +GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATGTGACTCCCCGTTGTAGACTACGATTAGACCCATCTCTCTGGCCACAGCTAACTCGCTCAACTCTCATCCCTCCTGGGGTATCTACCAGCGATACGCGTAGAACTCGTGCCTCATGC ++ +^^^^^aaaccccccccfeefffgggghggggggghgggghgabddgeeggghhgeggghhhhhhhgheafefegggghgd_dddggeeggee^begggggfffffffffffffffffffdbfffZddYbdfff^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAGNNCGCCGCTAAGACTGCCGTCAAATTCCTGAGCGGTAGTGATGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCGGGGGGCGCCGGCACATTCAAAAAAAAAAAACAGGAAAATGACATAGGCGTGTGTGA ++ +^^```aaacccccdccffbeffggheeggg>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>UU^\>>SUU__dddfbffb]bd[dfddfdfbdfdffffWW[^P^b^dfbd^ddb^bb^bbdffbffbfbW^bb`b[``EQQQW]HOHPbY^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCCGCCTACTTTCCCAAGGCGCGATAAAGATTGATGGAACCCCGCCCAAGGCTGACGAAATCCCCGCCAACGAACTGTCGGGCCGACCCATTCAAGTGGGGAAAAAAACCTTTCCCCGGGTTGACAAACCGCCAAACAACCTCACCAA ++ +^^^^Xa^^^`cX^accddccccgggggegegeegggggggggdgg]bdfggefggfgg\eggggbJbfdabb[be_KSbe_beaeeeece^aSac__cG]bdUaaGGMGMY```dd^`^`>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGAGCCTCTGCAACCAGCAGAGGTTGCCAAGCTGGACTATCACAGCTACGTCACCAGACGCTTCATGAAGGTCACCCAGTCTGACCCTGTGAACCAGGCCGGG ++ +`^^`^aaaccccccccffffffgdeggfdggghgdgggggcgadgfeeedffcddcfffffdffddbd^dfbdfdfffbdddffbddffScZZS`ffffffW]ff`^dfffddfddfffbffdfdffffcW[``cdbdbdff^bbbYWbbEEWYbY^bbdH^GObbOYH^YbY^bbbW^bbdbXHYYbbbb^bHYYMbdffdbXXbSEGGMOOHYbY^HPOYbb>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC +GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATTGAGAATCCGCTAGCGGATAAGATTTTGCGGGGGGAGTTGGCGGAGGGCGATCGCTTGATGCTTGATTATGGAGGGGAGGGGGAGAAGATAGGTTTTACGAAAATAGAGGCGGAGGGGTCGGCGGCATAGAGGGTAATTTTTTGGGTTTTTTTCTGTGTCTTATACACAACTGAACGTGCCGACGAGCGG ++ +^^^^^_^accccccccedddeeghhgdggggcgggggdggggggW`ceeeceecPcZ]PKZZZZRaKRaZZHYaZPZEEOYYOHPY`HYZ]ccESEWMYY``]cQQ]c`]EEOMMOW^HY`HP^YHO^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGAACAAG ++ +^^^^^aaaccccccccfbefefhhhhhgeghhhhghgef\dgghfhhhheghgcfgfggghghg\bfgffgegggegefggegN`bceff^ed^bceeggggghhgeggh]bdcfeggggggggceggegggee`eeffffffdcdf]]c`bbZ^dff]bdd`]`d`bbdd^YbYYbbYYYbYbd[b[XbY^b^H^bddbbbHYb^b^dY^YbYbYbbbbdY^bPHOHPPMWbGQ^ESW]f>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC +GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCGTCCTGGTTTGCGTCGGGGATGCGGTCACCCTCTAAAAGATTTATGGAGGTCGTCTCTTGTGTCTGGGCCGGGGGGAAGATGT ++ +^^^^^aaaccccccccffffffhhghheggghgghegfgffgghghhcdeegde_ceghhghhhfg`bcbeeggghghhghgfgggafefddggggegeeggcecbdffeffefff_caddddfb]bddffffffdO^bcfffc]ddQbdWbdfdd[]]]GYbddfc`ESQWbdY^XbbSWQW]ES[GOY]EOSGP^dHWYPbb^^GYbbddbbHHWGOTSW^bHY^YHOPOHYbb>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC +GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCCGTGGGCGCCGCATCATTAAAAAAAAAAAAAAAAAACATAACTCTCAAACGCGAATAGAGCAAGAAACAGACAGCTAAAGTACAAACAAT ++ +TT[^^^^^cccaaccaeeeeeebgghhgghhhhhhhgfgghhhhggfghhgegghhhhgggbcghhhgeeghhhhhbeeghgdbfbfdghg\eggggggggggeZeeeeecceeeeeeedeeeededace`dd`dd_ddcc]cccWWOY^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAGAGGAGGAGGAGAGAAGGGGGAATGAGCAAGTAACATAATTACATAGCTGTGTCTGAATCTCTTTGAGCACCCTACCTCGGCATAGGAGGCTAGCTGGTGAGGGAGGGAGGGGCAGACTGACAGGCCGAGGATGGCCTTGTGGTTGGCAAACTCCGTGGGGCGAGTCTGGGCTGCTGCATGCGCATCTGAGACTGGCTCTTGTACACATC ++ +^^^^^_X_a^a^aaaadddea__ddgdb^aeLbd_ccdgKTJTbK]_JbdJ[^\dLbedbdggcacK^ceeKScccaeZ\aZZaacZcKaS\adddddbaKKaaZ^b^bddddHZZbY`b^bZ^bbY`ddd^dW`bdYOY`^``W`SM^^W^WQSWGWY`bddd^dGSZ^Z^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_pe_r1_paired_out1.fastqillumina Fri Oct 05 05:19:17 2018 -0400 @@ -0,0 +1,32 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNT ++ +^^^^^aaa_aaaa^aaeeeeBU +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNA ++ +^^^^^aaacccc`cccd_eeBU +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGG ++ +^[K[^aaaaaaaaaaaeeeeBU`bdbbdbVWbd\bfgdgVbgbgefg`cfgggbbbggd[cegeeeeceeeeeecececcdddddddddb`ddddZ^adddaddabdZbZSWZ +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGGGCTCAGCGCTNT ++ +T\\\\]N[______]_bbbdBU +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGG ++ +^^K[^aaaccccccc[eee_ebZeeeadegggbccggfgggcfgggeggd`^dd`ddgcdegggggedbegggegcgddggbegVbdegcdggbeggegge\eeececeeeeddddccdeddd[aabdabdK\\`dPYY``ddbddI^I``dee^^]c^HW +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTA ++ +^^^^^aaaccccccccffffffhhhggeeggggggggggdggdggggghhgggggedghhhgghgghghghhhhhggggggggggggggggcggggggggfdcefffffffZbdfdfbdfffffW]ffffdffddbdffffcWdcff`dfddffbdYbffWbddff^^^bdd[cfWbbI^^]cfMW[`ffffbddfIbQ[fbbdbdIY^bd^bdXbYbYbY^b +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGG ++ +^^^^^aaacacccccceeeeeeghghgggggghgheffgegggghheghgg^ddfggggggLdfdggbdggggg_eceedeeT_dddeededZ`dbbdZ`ddddd`^W^`dccddceecdQ]]ddee[[[Q]c^cdddIYb^``[]W`debddY^b^ddd^bdeddO^Yd^`bddbcW]dd]HW]dYbddddddcMH^`d^^`^Y`^I^^YbO^bbd^```YWWMWW^YYbYb^IW +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGG ++ +\T\\\[]JT[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_pe_r1_paired_out1.fastqsolexa Fri Oct 05 05:19:17 2018 -0400 @@ -0,0 +1,32 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNT ++ +^^^^^aaa_aaaa^aaeeee>U +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNA ++ +^^^^^aaacccc`cccd_ee>U +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGG ++ +^[K[^aaaaaaaaaaaeeee>U`bdbbdbVWbd\bfgdgVbgbgefg`cfgggbbbggd[cegeeeeceeeeeecececcdddddddddb`ddddZ^adddaddabdZbZSWZ +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGGGCTCAGCGCTNT ++ +T\\\\]N[______]_bbbd>U +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTC ++ +^^K[^aaaccccccc[eee_ebZeeeadegggbccggfgggcfgggeggd`^dd`ddgcdegggggedbegggegcgddggbegVbdegcdggbeggegge\eeececeeeeddddccdeddd[aabdabdK\\`dPYY``ddbddH^ +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTA ++ +^^^^^aaaccccccccffffffhhhggeeggggggggggdggdggggghhgggggedghhhgghgghghghhhhhggggggggggggggggcggggggggfdcefffffffZbdfdfbdfffffW]ffffdffddbdffffcWdcff`dfddffbdYbffWbddff^^^bdd[cfWbbH^^]cfMW[`ffffbddfHbQ[fbbdbdHY^bd^bdXbYbYbY^b +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGG ++ +^^^^^aaacacccccceeeeeeghghgggggghgheffgegggghheghgg^ddfggggggLdfdggbdggggg_eceedeeT_dddeededZ`dbbdZ`ddddd`^W^`dccddceecdQ]]ddee[[[Q]c^cdddHYb^``[]W`debddY^b^ddd^bdeddO^Yd^`bddbcW]dd]GW]dYbddddddcMG^`d^^`^Y`^H^^YbO^bbd^```YWWMWW^YYbYb^HW +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGG ++ +\T\\\[]JT[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_pe_r2_paired_out1.fastqillumina Fri Oct 05 05:19:17 2018 -0400 @@ -0,0 +1,32 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC +GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAG ++ +^^`^^`aacccccccceedddeghhhhgghhgheghhgggegghhhhhgggegghhhhhheeegghhgfcdgg``dggggeggggc\daadddddeeeeddddbdeeddeeeWI^^``^Z]cdddeeeeI^W`dbedeeeeeed`dddbeeebdddeeeeeedded`bddb^b``bdeddded^O^d`b```dd``bdd` +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC +GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATG ++ +^^^^^aaaccccccccfeefffgggghggggggghgggghgabddgeeggghhgeggghhhhhhhgheafefegggghgd_dddggeeggee^begggggfffffffffffffffffffdbfffZddYbdfff^ +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACC ++ +^^```aaacccccdccffbeffggheeggg +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCC ++ +^^^^Xa^^^`cX^accddccccgggggegegeegggggggggdgg]bdfggefggfgg\eggggbJbfdabb[be_KSbe_beaeeeece^aSac__cH]bdUaa +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGA ++ +`^^`^aaaccccccccffffffgdeggfdggghgdgggggcgadgfeeedffcddcfffffdffddbd^dfbdfdfffbdddffbddffScZZS`ffffffW]ff`^dfffddfddfffbffdfdffffcW[``cdbdbdff^bbbYWbb +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC +GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATT ++ +^^^^^_^accccccccedddeeghhgdggggcgggggdggggggW`ceeeceecPcZ]PKZ +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC +GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCG ++ +^^^^^aaaccccccccffffffhhghheggghgghegfgffgghghhcdeegde_ceghhghhhfg`bcbeeggghghhghgfgggafefddggggegeeggcecbdffeffefff_caddddfb]bddffffffdO^bcfffc]ddQbdWbdfdd[]]]HYbddfc` +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC +GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAG ++ +TT[^^^^^cccaaccaeeeeeebgghhgghhhhhhhgfgghhhhggfghhgegghhhhgggbcghhhgeeghhhhhbeeghgdbfbfdghg\eggggggggggeZeeeeecceeeeeeedeeeededace`dd`dd_ddcc]cccWWOY^
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_pe_r2_paired_out1.fastqsolexa Fri Oct 05 05:19:17 2018 -0400 @@ -0,0 +1,32 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC +GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAG ++ +^^`^^`aacccccccceedddeghhhhgghhgheghhgggegghhhhhgggegghhhhhheeegghhgfcdgg``dggggeggggc\daadddddeeeeddddbdeeddeeeWH^^``^Z]cdddeeeeH^W`dbedeeeeeed`dddbeeebdddeeeeeedded`bddb^b``bdeddded^O^d`b```dd``bdd` +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC +GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATG ++ +^^^^^aaaccccccccfeefffgggghggggggghgggghgabddgeeggghhgeggghhhhhhhgheafefegggghgd_dddggeeggee^begggggfffffffffffffffffffdbfffZddYbdfff^ +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACC ++ +^^```aaacccccdccffbeffggheeggg +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCC ++ +^^^^Xa^^^`cX^accddccccgggggegegeegggggggggdgg]bdfggefggfgg\eggggbJbfdabb[be_KSbe_beaeeeece^aSac__cG]bdUaa +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGA ++ +`^^`^aaaccccccccffffffgdeggfdggghgdgggggcgadgfeeedffcddcfffffdffddbd^dfbdfdfffbdddffbddffScZZS`ffffffW]ff`^dfffddfddfffbffdfdffffcW[``cdbdbdff^bbbYWbb +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC +GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATT ++ +^^^^^_^accccccccedddeeghhgdggggcgggggdggggggW`ceeeceecPcZ]PKZ +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC +GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCG ++ +^^^^^aaaccccccccffffffhhghheggghgghegfgffgghghhcdeegde_ceghhghhhfg`bcbeeggghghhghgfgggafefddggggegeeggcecbdffeffefff_caddddfb]bddffffffdO^bcfffc]ddQbdWbdfdd[]]]GYbddfc` +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC +GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAG ++ +TT[^^^^^cccaaccaeeeeeebgghhgghhhhhhhgfgghhhhggfghhgegghhhhgggbcghhhgeeghhhhhbeeghgdbfbfdghg\eggggggggggeZeeeeecceeeeeeedeeeededace`dd`dd_ddcc]cccWWOY^
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_pe_r2_unpaired_out1.fastqillumina Fri Oct 05 05:19:17 2018 -0400 @@ -0,0 +1,8 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACA ++ +^^^^^aaaccccccccfbefefhhhhhgeghhhhghgef\dgghfhhhheghgcfgfggghghg\bfgffgegggegefggegN`bceff^ed^bceeggggghhgeggh]bdcfeggggggggceggegggee`eeffffffdcdf]]c`bbZ^dff]bdd`]`d`bbdd^YbYYbbYYYbYbd[b[XbY^b^I^bddbbbIYb^b^dY^YbYbYbbbbdY^b +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAG ++ +^^^^^_X_a^a^aaaadddea__ddgdb^aeLbd_ccdgKT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_pe_r2_unpaired_out1.fastqsolexa Fri Oct 05 05:19:17 2018 -0400 @@ -0,0 +1,8 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACA ++ +^^^^^aaaccccccccfbefefhhhhhgeghhhhghgef\dgghfhhhheghgcfgfggghghg\bfgffgegggegefggegN`bceff^ed^bceeggggghhgeggh]bdcfeggggggggceggegggee`eeffffffdcdf]]c`bbZ^dff]bdd`]`d`bbdd^YbYYbbYYYbYbd[b[XbY^b^H^bddbbbHYb^b^dY^YbYbYbbbbdY^b +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAG ++ +^^^^^_X_a^a^aaaadddea__ddgdb^aeLbd_ccdgKT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_se_out1.err Fri Oct 05 05:19:17 2018 -0400 @@ -0,0 +1,5 @@ +TrimmomaticSE: Started with arguments: + -threads 1 fastq_in.fastqsanger fastq_out.fastqsanger SLIDINGWINDOW:4:20 -trimlog trimlog +Quality encoding detected as phred33 +Input Reads: 10 Surviving: 8 (80.00%) Dropped: 2 (20.00%) +TrimmomaticSE: Completed successfully
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_se_out1.log Fri Oct 05 05:19:17 2018 -0400 @@ -0,0 +1,10 @@ +MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC 22 0 22 228 +MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC 22 0 22 228 +MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC 113 0 113 137 +MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC 22 0 22 228 +MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC 161 0 161 89 +MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC 223 0 223 27 +MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC 0 0 0 0 +MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC 236 0 236 14 +MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC 10 0 10 240 +MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC 0 0 0 0
--- a/trimmomatic.xml Mon Mar 05 10:13:48 2018 -0500 +++ b/trimmomatic.xml Fri Oct 05 05:19:17 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="trimmomatic" name="Trimmomatic" version="0.36.5"> +<tool id="trimmomatic" name="Trimmomatic" version="0.36.6"> <description>flexible read trimming tool for Illumina NGS data</description> <macros> <import>trimmomatic_macros.xml</import> @@ -24,12 +24,12 @@ #end if java \${_JAVA_OPTIONS:--Xmx8G} -jar \$TRIMMOMATIC_JAR_PATH/trimmomatic.jar #if $readtype.single_or_paired in ["pair_of_files","collection"] - PE -threads \${GALAXY_SLOTS:-6} -phred33 + PE -threads \${GALAXY_SLOTS:-6} fastq_r1.'$r1_ext' fastq_r2.'$r2_ext' fastq_out_r1_paired.'$r1_ext' fastq_out_r1_unpaired.'$r1_ext' fastq_out_r2_paired.'$r2_ext' fastq_out_r2_unpaired.'$r2_ext' #else - SE -threads \${GALAXY_SLOTS:-6} -phred33 fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension' + SE -threads \${GALAXY_SLOTS:-6} fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension' #end if ## ILLUMINACLIP option #if $illuminaclip.do_illuminaclip @@ -76,6 +76,9 @@ MAXINFO:$op.operation.target_length:$op.operation.strictness #end if #end for + #if $output_logs: + -trimlog trimlog + #end if 2>&1 | tee trimmomatic.log && if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && @@ -109,16 +112,16 @@ <option value="collection">Paired-end (as collection)</option> </param> <when value="se"> - <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ file" /> + <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file" /> </when> <when value="pair_of_files"> - <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz" + <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file (R1/first of pair)" /> - <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz" + <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file (R2/second of pair)" /> </when> <when value="collection"> - <param name="fastq_pair" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" /> + <param name="fastq_pair" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" /> </when> </conditional> <conditional name="illuminaclip"> @@ -198,6 +201,8 @@ </when> </conditional> </repeat> + <param name="output_logs" argument="-trimlog" type="boolean" label="Output trimlog file?" truevalue="yes" falsevalue="no" checked="False" /> + <param name="output_err" type="boolean" label="Output trimmomatic log messages?" truevalue="yes" falsevalue="no" checked="False" help="these are the messages written to stderr (eg. for use in MultiQC)" /> </inputs> <outputs> <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in"> @@ -225,15 +230,26 @@ <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/> <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/> </collection> - + <data name="log_file" format="txt" label="${tool.name} on ${on_string} (trimlog file)" from_work_dir="trimlog"> + <filter>output_logs</filter> + </data> + <data name="err_file" format="txt" label="${tool.name} on ${on_string} (log file)" from_work_dir="trimmomatic.log"> + <filter>output_err</filter> + </data> </outputs> <tests> <test> <!-- Single-end example --> - <param name="single_or_paired" value="se" /> - <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> + <conditional name="readtype"> + <param name="single_or_paired" value="se" /> + <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> + </conditional> <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> + <param name="output_logs" value="yes" /> + <param name="output_err" value="yes" /> <output name="fastq_out" file="trimmomatic_se_out1.fastq" /> + <output name="log_file" file="trimmomatic_se_out1.log" /> + <output name="err_file" file="trimmomatic_se_out1.err" /> </test> <test> <!-- Single-end example - gzipped --> @@ -265,6 +281,28 @@ <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> </test> <test> + <!-- Paired-end Illumina 1.3-1.7 quality encoding --> + <param name="single_or_paired" value="pair_of_files" /> + <param name="fastq_r1_in" value="Illumina_SG_R1.fastqillumina" ftype="fastqillumina" /> + <param name="fastq_r2_in" value="Illumina_SG_R2.fastqillumina" ftype="fastqillumina" /> + <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> + <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqillumina" /> + <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqillumina" /> + <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqillumina" /> + <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqillumina" /> + </test> + <test> + <!-- Paired-end Solexa quality encoding --> + <param name="single_or_paired" value="pair_of_files" /> + <param name="fastq_r1_in" value="Illumina_SG_R1.fastqsolexa" ftype="fastqsolexa" /> + <param name="fastq_r2_in" value="Illumina_SG_R2.fastqsolexa" ftype="fastqsolexa" /> + <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> + <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqsolexa" /> + <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqsolexa" /> + <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqsolexa" /> + <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqsolexa" /> + </test> + <test> <!-- Single-end example (cropping) --> <param name="single_or_paired" value="se" /> <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> @@ -435,7 +473,7 @@ This Galaxy tool has been developed within the Bioinformatics Core Facility at the University of Manchester, with contributions from Peter van Heusden, Marius -van den Beek, Jelle Scholtalbers and Charles Girardot. +van den Beek, Jelle Scholtalbers, Charles Girardot, and Matthias Bernt. It runs the Trimmomatic program which has been developed within Bjorn Usadel's group at RWTH Aachen university.