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comparison bismark_bowtie2_wrapper.xml @ 0:36d124f44c0a draft

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date Tue, 25 Dec 2012 05:45:46 -0500
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1 <tool id="bismark_bowtie2" name="Bismark" version="0.7.7.2">
2 <!-- Wrapper compatible with Bismark version 0.7.7 -->
3 <description>bisulfite mapper (bowtie2)</description>
4 <!--<version_command>bismark version</version_command>-->
5 <requirements>
6 <requirement type="set_environment">SCRIPT_PATH</requirement>
7 <requirement type="package" version="0.12.8">bowtie</requirement>
8 <requirement type="package" version="2.0.0-beta7">bowtie2</requirement>
9 </requirements>
10 <parallelism method="basic"></parallelism>
11 <command interpreter="python">
12 bismark_wrapper.py
13
14 ## Change this to accommodate the number of threads you have available.
15 --num-threads 4
16
17 --bismark_path \$SCRIPT_PATH
18
19 --bowtie2
20
21 ##
22 ## Bismark Genome Preparation, if desired.
23 ##
24
25 ## Handle reference file.
26 #if $refGenomeSource.genomeSource == "history":
27 --own-file=$refGenomeSource.ownFile
28 #else:
29 --indexes-path ${refGenomeSource.index.fields.path}
30 #end if
31
32
33 ##
34 ## Input parameters
35 ##
36
37
38 #if $singlePaired.sPaired == "single":
39 --single-paired $singlePaired.input_singles
40
41 #if $singlePaired.input_singles.ext == "fastqillumina":
42 --phred64-quals
43 --fastq
44 #elif $singlePaired.input_singles.ext == "fastqsanger":
45 --fastq
46 #elif $singlePaired.input_singles.ext == "fasta":
47 --fasta
48 #end if
49 #else:
50 --mate-paired
51 --mate1 $singlePaired.input_mate1
52 --mate2 $singlePaired.input_mate2
53
54 #if $singlePaired.input_mate1.ext == "fastqillumina":
55 --phred64-quals
56 --fastq
57 #elif $singlePaired.input_mate1.ext == "fastqsanger":
58 --fastq
59 #elif $singlePaired.input_mate1.ext == "fasta":
60 --fasta
61 #end if
62
63 -I $singlePaired.minInsert
64 -X $singlePaired.maxInsert
65 #end if
66
67
68 ## for now hardcode the value for the required memory per thread in --best mode
69 --chunkmbs 512
70
71
72 #if $params.settingsType == "custom":
73
74 ## default 20
75 --seed-len $params.seed_len
76 ## default 0
77 --seed-mismatches $params.seed_mismatches
78 ## default 15
79 --seed-extention-attempts $params.seed_extention_attempts
80 ## default 2
81 --max-reseed $params.max_reseed
82
83 ## default 70
84 ##--maqerr $params.maqerr
85
86 ## default unlimited
87 #if $params.qupto != 0:
88 --qupto $params.qupto
89 #end if
90 #if $params.skip_reads != 0:
91 --skip-reads $params.skip_reads
92 #end if
93
94 ## if set, disable the original behaviour
95 $params.no_mixed
96 ## if set, disable the original behaviour
97 $params.no_discordant
98
99
100 ###if str($params.isReportOutput) == "yes":
101 ## --output-report-file $report_file
102 ###end if
103
104 #end if
105
106 ##
107 ## Output parameters.
108 ##
109 --output $output
110 $suppress_header
111
112 #if str( $singlePaired.sPaired ) == "single"
113 #if $output_unmapped_reads_l
114 --output-unmapped-reads $output_unmapped_reads_l
115 #end if
116 #if $output_suppressed_reads_l
117 --output-suppressed-reads $output_suppressed_reads_l
118 #end if
119 #else
120 #if $output_unmapped_reads_l and $output_unmapped_reads_r
121 --output-unmapped-reads-l $output_unmapped_reads_l
122 --output-unmapped-reads-r $output_unmapped_reads_r
123 #end if
124 #if $output_suppressed_reads_l and $output_suppressed_reads_l
125 --output-suppressed-reads-l $output_suppressed_reads_l
126 --output-suppressed-reads-r $output_suppressed_reads_r
127 #end if
128 #end if
129
130 </command>
131 <inputs>
132 <conditional name="refGenomeSource">
133 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
134 <option value="indexed">Use a built-in index</option>
135 <option value="history">Use one from the history</option>
136 </param>
137 <when value="indexed">
138 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
139 <options from_data_table="bowtie2_indexes">
140 <filter type="sort_by" column="2"/>
141 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
142 </options>
143 </param>
144 </when> <!-- build-in -->
145 <when value="history">
146 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
147 </when> <!-- history -->
148 </conditional> <!-- refGenomeSource -->
149
150 <!-- Input Parameters -->
151 <conditional name="singlePaired">
152 <param name="sPaired" type="select" label="Is this library mate-paired?">
153 <option value="single">Single-end</option>
154 <option value="paired">Paired-end</option>
155 </param>
156 <when value="single">
157 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
158 </when>
159 <when value="paired">
160 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
161 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
162 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
163 <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" />
164 </when>
165 </conditional>
166
167
168 <conditional name="params">
169 <param name="settingsType" type="select" label="Bismark settings to use" help="You can use the default settings or set custom values for any of Bismark's parameters.">
170 <option value="default">Use Defaults</option>
171 <option value="custom">Full parameter list</option>
172 </param>
173 <when value="default" />
174 <!-- Full/advanced params. -->
175 <when value="custom">
176 <!-- -N -->
177 <param name="seed_mismatches" type="integer" value="0" label="Number of mismatches to be allowed in a seed alignment during multiseed alignment" />
178 <!-- -L -->
179 <param name="seed_len" type="integer" value="20" label="Length of the seed substrings to align during multiseed alignment" />
180 <!--
181 <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the 'seed'." />
182 -->
183 <!-- -D -->
184 <param name="seed_extention_attempts" type="integer" value="15" label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on" />
185 <!-- -R -->
186 <param name="max_reseed" type="integer" value="2" label="Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds" />
187
188 <param name="qupto" type="integer" value="0" label="Only aligns the first N reads or read pairs from the input" help="Default is 0 and means 'no-limit'." />
189 <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input" />
190
191 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable looking for discordant alignments if it cannot find any concordant alignments" help="" />
192 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates" help="" />
193
194 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write ambiguous reads to an extra output file." help="Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely." />
195 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file" />
196 <!-- output Options -->
197 <!--
198 <param name="isReportOutput" type="select" label="Offer all report files concatenated in one file.">
199 <option value="yes">yes</option>
200 <option value="no">no</option>
201 </param>
202 -->
203 <!--end output options -->
204 </when> <!-- full -->
205 </conditional> <!-- params -->
206 <param name="suppress_header" type="boolean" truevalue="--suppress-header" falsevalue="" checked="False" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" />
207 </inputs>
208 <outputs>
209 <!-- that does not work
210 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: Report">
211 <filter>str($params.isReportOutput) == "yes"</filter>
212 </data>
213 -->
214 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
215 <actions>
216 <conditional name="refGenomeSource.genomeSource">
217 <when value="indexed">
218 <action type="metadata" name="dbkey">
219 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
220 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
221 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
222 </option>
223 </action>
224 </when>
225 <when value="history">
226 <action type="metadata" name="dbkey">
227 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
228 </action>
229 </when>
230 </conditional>
231 </actions>
232 </data>
233
234 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
235 <filter>
236 ((
237 params['settingsType'] == "custom" and
238 params['suppressed_read_file'] is True
239 ))
240 </filter>
241 <actions>
242 <conditional name="singlePaired.sPaired">
243 <when value="single">
244 <action type="format">
245 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
246 </action>
247 </when>
248 <when value="paired">
249 <action type="format">
250 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
251 </action>
252 </when>
253 </conditional>
254 </actions>
255 </data>
256
257 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
258 <filter>singlePaired['sPaired'] == "paired"</filter>
259 <filter>params['settingsType'] == "custom"</filter>
260 <filter>params['supressed_read_file'] is True</filter>
261 <actions>
262 <conditional name="singlePaired.sPaired">
263 <when value="single">
264 <action type="format">
265 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
266 </action>
267 </when>
268 <when value="paired">
269 <action type="format">
270 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
271 </action>
272 </when>
273 </conditional>
274 </actions>
275 </data>
276
277 <!-- Outout unmapped reads -->
278 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
279 <filter>
280 ((
281 params['settingsType'] == "custom" and
282 params['unmapped_read_file'] is True
283 ))
284 </filter>
285 <actions>
286 <conditional name="singlePaired.sPaired">
287 <when value="single">
288 <action type="format">
289 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
290 </action>
291 </when>
292 <when value="paired">
293 <action type="format">
294 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
295 </action>
296 </when>
297 </conditional>
298 </actions>
299 </data>
300 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
301 <filter>singlePaired['sPaired'] == "paired"</filter>
302 <filter>params['settingsType'] == "custom"</filter>
303 <filter>params['unmapped_read_file'] is True</filter>
304 <actions>
305 <conditional name="singlePaired.sPaired">
306 <when value="single">
307 <action type="format">
308 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
309 </action>
310 </when>
311 <when value="paired">
312 <action type="format">
313 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
314 </action>
315 </when>
316 </conditional>
317 </actions>
318 </data>
319
320
321 </outputs>
322
323 <tests>
324 </tests>
325
326 <help>
327
328 **What it does**
329
330 Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the
331 reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand
332 version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand).
333 Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome
334 (C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the
335 forward strand, by doing this alignments will produce the same positions). These 4 instances of Bowtie (1 or 2)
336 are run in parallel. The sequence file(s) are then read in again sequence by sequence to pull out the original
337 sequence from the genome and determine if there were any protected C's present or not.
338
339 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
340
341 As of version 0.7.0 Bismark will only run 2 alignment threads for OT and OB in parallel, the 4 strand mode can be
342 re-enabled by using non_directional mode.
343
344 It is developed by Krueger F and Andrews SR. at the Babraham Institute. Krueger F, Andrews SR. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-2.
345
346 ------
347
348 **Know what you are doing**
349
350 .. class:: warningmark
351
352 There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
353
354 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
355
356 ------
357
358 **Input formats**
359
360 Bismark accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*), Illumina FASTQ format (galaxy type *fastqillumina*) or FASTA format (galaxy type *fasta*). Use the FASTQ Groomer to prepare your files.
361
362 ------
363
364 **A Note on Built-in Reference Genomes**
365
366 The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
367
368 ------
369
370 The final output of Bismark is in SAM format by default.
371
372 **Outputs**
373
374 The output is in SAM format, and has the following columns::
375
376 Column Description
377 -------- --------------------------------------------------------
378 1 QNAME seq-ID
379 2 FLAG this flag tries to take the strand a bisulfite read
380 originated from into account
381 (this is different from ordinary DNA alignment flags!)
382 3 RNAME chromosome
383 4 POS start position
384 5 MAPQ always 255
385 6 CIGAR extended CIGAR string
386 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
387 8 MPOS 1-based Mate POSition
388 9 ISIZE Inferred insert SIZE
389 10 SEQ query SEQuence on the same strand as the reference
390 11 QUAL Phred33 scale
391 12 NM-tag edit distance to the reference)
392 13 XX-tag base-by-base mismatches to the reference.
393 This does not include indels.
394 14 XM-tag methylation call string
395 15 XR-tag read conversion state for the alignment
396 16 XG-tag genome conversion state for the alignment
397
398
399 Each read of paired-end alignments is written out in a separate line in the above format.
400
401
402 It looks like this (scroll sideways to see the entire example)::
403
404 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
405 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
406 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
407
408 -------
409
410 **Bismark settings**
411
412 All of the options have a default value. You can change any of them. If any Bismark function is missing please contact the tool author or your Galaxy admin.
413
414 ------
415
416 **Bismark parameter list**
417
418 This is an exhaustive list of Bismark options:
419
420 ------
421
422 **OPTIONS**
423
424
425 Input::
426
427 --singles A comma- or space-separated list of files containing the reads to be aligned (e.g.
428 lane1.fq,lane2.fq lane3.fq). Reads may be a mix of different lengths. Bismark will
429 produce one mapping result and one report file per input file.
430
431 -1 mates1 Comma-separated list of files containing the #1 mates (filename usually includes
432 "_1"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
433 correspond file-for-file and read-for-read with those specified in mates2.
434 Reads may be a mix of different lengths. Bismark will produce one mapping result
435 and one report file per paired-end input file pair.
436
437 -2 mates2 Comma-separated list of files containing the #2 mates (filename usually includes
438 "_2"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
439 correspond file-for-file and read-for-read with those specified in mates1.
440 Reads may be a mix of different lengths.
441
442 -q/--fastq The query input files (specified as mate1,mate2 or singles are FASTQ
443 files (usually having extension .fg or .fastq). This is the default. See also
444 --solexa-quals.
445
446 -f/--fasta The query input files (specified as mate1,mate2 or singles are FASTA
447 files (usually havin extension .fa, .mfa, .fna or similar). All quality values
448 are assumed to be 40 on the Phred scale.
449
450 -s/--skip INT Skip (i.e. do not align) the first INT reads or read pairs from the input.
451
452 -u/--upto INT Only aligns the first INT reads or read pairs from the input. Default: no limit.
453
454 --phred33-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 33. Default: on.
455
456 --phred64-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off.
457
458 --solexa-quals Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled
459 (which can't). The formula for conversion is:
460 phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This
461 is usually the right option for use with (unconverted) reads emitted by the GA
462 Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off.
463
464 --solexa1.3-quals Same as --phred64-quals. This is usually the right option for use with (unconverted)
465 reads emitted by GA Pipeline version 1.3 or later. Default: off.
466
467
468 Alignment::
469
470 -n/--seedmms INT The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs
471 of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the
472 default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N).
473
474 -l/--seedlen The "seed length"; i.e., the number of bases of the high quality end of the read to
475 which the -n ceiling applies. The default is 28. Bowtie (and thus Bismark) is faster for
476 larger values of -l. This option is only available for Bowtie 1 (for Bowtie 2 see -L).
477
478 -e/--maqerr INT Maximum permitted total of quality values at all mismatched read positions throughout
479 the entire alignment, not just in the "seed". The default is 70. Like Maq, bowtie rounds
480 quality values to the nearest 10 and saturates at 30. This value is not relevant for
481 Bowtie 2.
482
483 --chunkmbs INT The number of megabytes of memory a given thread is given to store path descriptors in
484 --best mode. Best-first search must keep track of many paths at once to ensure it is
485 always extending the path with the lowest cumulative cost. Bowtie tries to minimize the
486 memory impact of the descriptors, but they can still grow very large in some cases. If
487 you receive an error message saying that chunk memory has been exhausted in --best mode,
488 try adjusting this parameter up to dedicate more memory to the descriptors. This value
489 is not relevant for Bowtie 2. Default: 512.
490
491 -I/--minins INT The minimum insert size for valid paired-end alignments. E.g. if -I 60 is specified and
492 a paired-end alignment consists of two 20-bp alignments in the appropriate orientation
493 with a 20-bp gap between them, that alignment is considered valid (as long as -X is also
494 satisfied). A 19-bp gap would not be valid in that case. Default: 0.
495
496 -X/--maxins INT The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and
497 a paired-end alignment consists of two 20-bp alignments in the proper orientation with a
498 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied).
499 A 61-bp gap would not be valid in that case. Default: 500.
500
501
502
503 Output::
504
505 --non_directional The sequencing library was constructed in a non strand-specific manner, alignments to all four
506 bisulfite strands will be reported. Default: OFF.
507
508 (The current Illumina protocol for BS-Seq is directional, in which case the strands complementary
509 to the original strands are merely theoretical and should not exist in reality. Specifying directional
510 alignments (which is the default) will only run 2 alignment threads to the original top (OT)
511 or bottom (OB) strands in parallel and report these alignments. This is the recommended option
512 for sprand-specific libraries).
513
514 --sam-no-hd Suppress SAM header lines (starting with @). This might be useful when very large input files are
515 split up into several smaller files to run concurrently and the output files are to be merged.
516
517 --quiet Print nothing besides alignments.
518
519 --vanilla Performs bisulfite mapping with Bowtie 1 and prints the 'old' output (as in Bismark 0.5.X) instead
520 of SAM format output.
521
522 -un/--unmapped Write all reads that could not be aligned to a file in the output directory. Written reads will
523 appear as they did in the input, without any translation of quality values that may have
524 taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1
525 and _2 inserted in their filenames, i.e. _unmapped_reads_1.txt and unmapped_reads_2.txt. Reads
526 with more than one valid alignment with the same number of lowest mismatches (ambiguous mapping)
527 are also written to _unmapped_reads.txt unless the option --ambiguous is specified as well.
528
529 --ambiguous Write all reads which produce more than one valid alignment with the same number of lowest
530 mismatches or other reads that fail to align uniquely to a file in the output directory.
531 Written reads will appear as they did in the input, without any of the translation of quality
532 values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two
533 parallel files with _1 and _2 inserted in theit filenames, i.e. _ambiguous_reads_1.txt and
534 _ambiguous_reads_2.txt. These reads are not written to the file specified with --un.
535
536 -o/--output_dir DIR Write all output files into this directory. By default the output files will be written into
537 the same folder as the input file(s). If the specified folder does not exist, Bismark will attempt
538 to create it first. The path to the output folder can be either relative or absolute.
539
540 --temp_dir DIR Write temporary files to this directory instead of into the same directory as the input files. If
541 the specified folder does not exist, Bismark will attempt to create it first. The path to the
542 temporary folder can be either relative or absolute.
543
544 ------
545
546 Bowtie 2 alignment options::
547
548 -N INT Sets the number of mismatches to allowed in a seed alignment during multiseed alignment.
549 Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower)
550 but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for
551 Bowtie 1 see -n).
552
553 -L INT Sets the length of the seed substrings to align during multiseed alignment. Smaller values
554 make alignment slower but more senstive. Default: the --sensitive preset of Bowtie 2 is
555 used by default, which sets -L to 20. This option is only available for Bowtie 2 (for
556 Bowtie 1 see -l).
557
558 --ignore-quals When calculating a mismatch penalty, always consider the quality value at the mismatched
559 position to be the highest possible, regardless of the actual value. I.e. input is treated
560 as though all quality values are high. This is also the default behavior when the input
561 doesn't specify quality values (e.g. in -f mode). This option is invariable and on by default.
562
563
564 Bowtie 2 paired-end options::
565
566 --no-mixed This option disables Bowtie 2's behavior to try to find alignments for the individual mates if
567 it cannot find a concordant or discordant alignment for a pair. This option is invariable and
568 and on by default.
569
570 --no-discordant Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments.
571 A discordant alignment is an alignment where both mates align uniquely, but that does not
572 satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior
573 and it is on by default.
574
575
576 Bowtie 2 effort options::
577
578 -D INT Up to INT consecutive seed extension attempts can "fail" before Bowtie 2 moves on, using
579 the alignments found so far. A seed extension "fails" if it does not yield a new best or a
580 new second-best alignment. Default: 15.
581
582 -R INT INT is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds.
583 When "re-seeding," Bowtie 2 simply chooses a new set of reads (same length, same number of
584 mismatches allowed) at different offsets and searches for more alignments. A read is considered
585 to have repetitive seeds if the total number of seed hits divided by the number of seeds
586 that aligned at least once is greater than 300. Default: 2.
587
588
589 Bowtie 2 Scoring options::
590
591 --score_min "func" Sets a function governing the minimum alignment score needed for an alignment to be considered
592 "valid" (i.e. good enough to report). This is a function of read length. For instance, specifying
593 L,0,-0.2 sets the minimum-score function f to f(x) = 0 + -0.2 * x, where x is the read length.
594 See also: setting function options at http://bowtie-bio.sourceforge.net/bowtie2. The default is
595 L,0,-0.2.
596
597
598 Bowtie 2 Reporting options::
599
600 --most_valid_alignments INT This used to be the Bowtie 2 parameter -M. As of Bowtie 2 version 2.0.0 beta7 the option -M is
601 deprecated. It will be removed in subsequent versions. What used to be called -M mode is still the
602 default mode, but adjusting the -M setting is deprecated. Use the -D and -R options to adjust the
603 effort expended to find valid alignments.
604
605 For reference, this used to be the old (now deprecated) description of -M:
606 Bowtie 2 searches for at most INT+1 distinct, valid alignments for each read. The search terminates when it
607 can't find more distinct valid alignments, or when it finds INT+1 distinct alignments, whichever
608 happens first. Only the best alignment is reported. Information from the other alignments is used to
609 estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. Increasing -M makes
610 Bowtie 2 slower, but increases the likelihood that it will pick the correct alignment for a read that
611 aligns many places. For reads that have more than INT+1 distinct, valid alignments, Bowtie 2 does not
612 guarantee that the alignment reported is the best possible in terms of alignment score. -M is
613 always used and its default value is set to 10.
614
615 </help>
616 </tool>