comparison bismark_bowtie_wrapper.xml @ 3:7eefe5d6eecd draft

reupload
author bjoern-gruening
date Tue, 25 Dec 2012 05:54:01 -0500
parents 36d124f44c0a
children 427fb56f2e41
comparison
equal deleted inserted replaced
2:371bb57ac729 3:7eefe5d6eecd
1 <tool id="bismark_bowtie" name="Bismark" version="0.7.7.2">
2 <!-- Wrapper compatible with Bismark version 0.7.7 -->
3 <description>bisulfite mapper (bowtie)</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 ##
20 ## Bismark Genome Preparation, if desired.
21 ##
22
23 ## Handle reference file.
24 #if $refGenomeSource.genomeSource == "history":
25 --own-file=$refGenomeSource.ownFile
26 #else:
27 --indexes-path ${refGenomeSource.index.fields.path}
28 #end if
29
30
31 ##
32 ## Input parameters
33 ##
34
35
36 #if $singlePaired.sPaired == "single":
37 --single-paired $singlePaired.input_singles
38
39 #if $singlePaired.input_singles.ext == "fastqillumina":
40 --phred64-quals
41 --fastq
42 #elif $singlePaired.input_singles.ext == "fastqsanger":
43 --fastq
44 #elif $singlePaired.input_singles.ext == "fasta":
45 --fasta
46 #end if
47 #else:
48 --mate-paired
49 --mate1 $singlePaired.input_mate1
50 --mate2 $singlePaired.input_mate2
51
52 #if $singlePaired.input_mate1.ext == "fastqillumina":
53 --phred64-quals
54 --fastq
55 #elif $singlePaired.input_mate1.ext == "fastqsanger":
56 --fastq
57 #elif $singlePaired.input_mate1.ext == "fasta":
58 --fasta
59 #end if
60
61 -I $singlePaired.minInsert
62 -X $singlePaired.maxInsert
63 #end if
64
65
66 ## for now hardcode the value for the required memory per thread in --best mode
67 --chunkmbs 512
68
69
70 #if $params.settingsType == "custom":
71
72 ## default 20
73 --seed-len $params.seed_len
74 ## default 0
75 --seed-mismatches $params.seed_mismatches
76 ## default 15
77 --seed-extention-attempts $params.seed_extention_attempts
78 ## default 2
79 --max-reseed $params.max_reseed
80
81 ## default 70
82 ##--maqerr $params.maqerr
83
84 ## default unlimited
85 #if $params.qupto != 0:
86 --qupto $params.qupto
87 #end if
88 #if $params.skip_reads != 0:
89 --skip-reads $params.skip_reads
90 #end if
91
92 ## if set, disable the original behaviour
93 $params.no_mixed
94 ## if set, disable the original behaviour
95 $params.no_discordant
96
97
98 ###if str($params.isReportOutput) == "yes":
99 ## --output-report-file $report_file
100 ###end if
101
102 #end if
103
104 ##
105 ## Output parameters.
106 ##
107 --output $output
108 $suppress_header
109
110 #if str( $singlePaired.sPaired ) == "single"
111 #if $output_unmapped_reads_l
112 --output-unmapped-reads $output_unmapped_reads_l
113 #end if
114 #if $output_suppressed_reads_l
115 --output-suppressed-reads $output_suppressed_reads_l
116 #end if
117 #else
118 #if $output_unmapped_reads_l and $output_unmapped_reads_r
119 --output-unmapped-reads-l $output_unmapped_reads_l
120 --output-unmapped-reads-r $output_unmapped_reads_r
121 #end if
122 #if $output_suppressed_reads_l and $output_suppressed_reads_l
123 --output-suppressed-reads-l $output_suppressed_reads_l
124 --output-suppressed-reads-r $output_suppressed_reads_r
125 #end if
126 #end if
127
128 </command>
129 <inputs>
130 <conditional name="refGenomeSource">
131 <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">
132 <option value="indexed">Use a built-in index</option>
133 <option value="history">Use one from the history</option>
134 </param>
135 <when value="indexed">
136 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
137 <options from_data_table="bowtie_indexes">
138 <filter type="sort_by" column="2"/>
139 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
140 </options>
141 </param>
142 </when> <!-- build-in -->
143 <when value="history">
144 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
145 </when> <!-- history -->
146 </conditional> <!-- refGenomeSource -->
147
148 <!-- Input Parameters -->
149 <conditional name="singlePaired">
150 <param name="sPaired" type="select" label="Is this library mate-paired?">
151 <option value="single">Single-end</option>
152 <option value="paired">Paired-end</option>
153 </param>
154 <when value="single">
155 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
156 </when>
157 <when value="paired">
158 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
159 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
160 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
161 <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" />
162 </when>
163 </conditional>
164
165
166 <conditional name="params">
167 <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.">
168 <option value="default">Use Defaults</option>
169 <option value="custom">Full parameter list</option>
170 </param>
171 <when value="default" />
172 <!-- Full/advanced params. -->
173 <when value="custom">
174 <!-- -n -->
175 <param name="seed_mismatches" type="select" label="The maximum number of mismatches permitted in the 'seed'.">
176 <option value="0">0</option>
177 <option value="1">1</option>
178 <option value="2" selected="true">2</option>
179 <option value="3">3</option>
180 </param>
181 <!-- -l -->
182 <param name="seed_len" type="integer" value="28" label="The 'seed length'; The number of bases of the high quality end of the read to which the maximum number of mismatches applies." />
183 <!--
184 <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'." />
185 -->
186 <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'." />
187 <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" />
188
189 <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="" />
190 <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="" />
191
192 <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." />
193 <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" />
194 <!-- output Options -->
195 <!--
196 <param name="isReportOutput" type="select" label="Offer all report files concatenated in one file.">
197 <option value="yes">yes</option>
198 <option value="no">no</option>
199 </param>
200 -->
201 <!--end output options -->
202 </when> <!-- full -->
203 </conditional> <!-- params -->
204 <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" />
205 </inputs>
206 <outputs>
207 <!-- that does not work
208 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: Report">
209 <filter>str($params.isReportOutput) == "yes"</filter>
210 </data>
211 -->
212 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
213 <actions>
214 <conditional name="refGenomeSource.genomeSource">
215 <when value="indexed">
216 <action type="metadata" name="dbkey">
217 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
218 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
219 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
220 </option>
221 </action>
222 </when>
223 <when value="history">
224 <action type="metadata" name="dbkey">
225 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
226 </action>
227 </when>
228 </conditional>
229 </actions>
230 </data>
231
232 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
233 <filter>
234 ((
235 params['settingsType'] == "custom" and
236 params['suppressed_read_file'] is True
237 ))
238 </filter>
239 <actions>
240 <conditional name="singlePaired.sPaired">
241 <when value="single">
242 <action type="format">
243 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
244 </action>
245 </when>
246 <when value="paired">
247 <action type="format">
248 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
249 </action>
250 </when>
251 </conditional>
252 </actions>
253 </data>
254
255 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
256 <filter>singlePaired['sPaired'] == "paired"</filter>
257 <filter>params['settingsType'] == "custom"</filter>
258 <filter>params['supressed_read_file'] is True</filter>
259 <actions>
260 <conditional name="singlePaired.sPaired">
261 <when value="single">
262 <action type="format">
263 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
264 </action>
265 </when>
266 <when value="paired">
267 <action type="format">
268 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
269 </action>
270 </when>
271 </conditional>
272 </actions>
273 </data>
274
275 <!-- Outout unmapped reads -->
276 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
277 <filter>
278 ((
279 params['settingsType'] == "custom" and
280 params['unmapped_read_file'] is True
281 ))
282 </filter>
283 <actions>
284 <conditional name="singlePaired.sPaired">
285 <when value="single">
286 <action type="format">
287 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
288 </action>
289 </when>
290 <when value="paired">
291 <action type="format">
292 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
293 </action>
294 </when>
295 </conditional>
296 </actions>
297 </data>
298 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
299 <filter>singlePaired['sPaired'] == "paired"</filter>
300 <filter>params['settingsType'] == "custom"</filter>
301 <filter>params['unmapped_read_file'] is True</filter>
302 <actions>
303 <conditional name="singlePaired.sPaired">
304 <when value="single">
305 <action type="format">
306 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
307 </action>
308 </when>
309 <when value="paired">
310 <action type="format">
311 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
312 </action>
313 </when>
314 </conditional>
315 </actions>
316 </data>
317
318
319 </outputs>
320
321 <tests>
322 </tests>
323
324 <help>
325
326 **What it does**
327
328 Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the
329 reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand
330 version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand).
331 Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome
332 (C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the
333 forward strand, by doing this alignments will produce the same positions). These 4 instances of Bowtie (1 or 2)
334 are run in parallel. The sequence file(s) are then read in again sequence by sequence to pull out the original
335 sequence from the genome and determine if there were any protected C's present or not.
336
337 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
338
339 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
340 re-enabled by using non_directional mode.
341
342 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.
343
344 ------
345
346 **Know what you are doing**
347
348 .. class:: warningmark
349
350 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.
351
352 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
353
354 ------
355
356 **Input formats**
357
358 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.
359
360 ------
361
362 **A Note on Built-in Reference Genomes**
363
364 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.
365
366 ------
367
368 The final output of Bismark is in SAM format by default.
369
370 **Outputs**
371
372 The output is in SAM format, and has the following columns::
373
374 Column Description
375 -------- --------------------------------------------------------
376 1 QNAME seq-ID
377 2 FLAG this flag tries to take the strand a bisulfite read
378 originated from into account
379 (this is different from ordinary DNA alignment flags!)
380 3 RNAME chromosome
381 4 POS start position
382 5 MAPQ always 255
383 6 CIGAR extended CIGAR string
384 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
385 8 MPOS 1-based Mate POSition
386 9 ISIZE Inferred insert SIZE
387 10 SEQ query SEQuence on the same strand as the reference
388 11 QUAL Phred33 scale
389 12 NM-tag edit distance to the reference)
390 13 XX-tag base-by-base mismatches to the reference.
391 This does not include indels.
392 14 XM-tag methylation call string
393 15 XR-tag read conversion state for the alignment
394 16 XG-tag genome conversion state for the alignment
395
396
397 Each read of paired-end alignments is written out in a separate line in the above format.
398
399
400 It looks like this (scroll sideways to see the entire example)::
401
402 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
403 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
404 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
405
406 -------
407
408 **Bismark settings**
409
410 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.
411
412 ------
413
414 **Bismark parameter list**
415
416 This is an exhaustive list of Bismark options:
417
418 ------
419
420 **OPTIONS**
421
422
423 Input::
424
425 --singles A comma- or space-separated list of files containing the reads to be aligned (e.g.
426 lane1.fq,lane2.fq lane3.fq). Reads may be a mix of different lengths. Bismark will
427 produce one mapping result and one report file per input file.
428
429 -1 mates1 Comma-separated list of files containing the #1 mates (filename usually includes
430 "_1"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
431 correspond file-for-file and read-for-read with those specified in mates2.
432 Reads may be a mix of different lengths. Bismark will produce one mapping result
433 and one report file per paired-end input file pair.
434
435 -2 mates2 Comma-separated list of files containing the #2 mates (filename usually includes
436 "_2"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
437 correspond file-for-file and read-for-read with those specified in mates1.
438 Reads may be a mix of different lengths.
439
440 -q/--fastq The query input files (specified as mate1,mate2 or singles are FASTQ
441 files (usually having extension .fg or .fastq). This is the default. See also
442 --solexa-quals.
443
444 -f/--fasta The query input files (specified as mate1,mate2 or singles are FASTA
445 files (usually havin extension .fa, .mfa, .fna or similar). All quality values
446 are assumed to be 40 on the Phred scale.
447
448 -s/--skip INT Skip (i.e. do not align) the first INT reads or read pairs from the input.
449
450 -u/--upto INT Only aligns the first INT reads or read pairs from the input. Default: no limit.
451
452 --phred33-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 33. Default: on.
453
454 --phred64-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off.
455
456 --solexa-quals Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled
457 (which can't). The formula for conversion is:
458 phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This
459 is usually the right option for use with (unconverted) reads emitted by the GA
460 Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off.
461
462 --solexa1.3-quals Same as --phred64-quals. This is usually the right option for use with (unconverted)
463 reads emitted by GA Pipeline version 1.3 or later. Default: off.
464
465
466 Alignment::
467
468 -n/--seedmms INT The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs
469 of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the
470 default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N).
471
472 -l/--seedlen The "seed length"; i.e., the number of bases of the high quality end of the read to
473 which the -n ceiling applies. The default is 28. Bowtie (and thus Bismark) is faster for
474 larger values of -l. This option is only available for Bowtie 1 (for Bowtie 2 see -L).
475
476 -e/--maqerr INT Maximum permitted total of quality values at all mismatched read positions throughout
477 the entire alignment, not just in the "seed". The default is 70. Like Maq, bowtie rounds
478 quality values to the nearest 10 and saturates at 30. This value is not relevant for
479 Bowtie 2.
480
481 --chunkmbs INT The number of megabytes of memory a given thread is given to store path descriptors in
482 --best mode. Best-first search must keep track of many paths at once to ensure it is
483 always extending the path with the lowest cumulative cost. Bowtie tries to minimize the
484 memory impact of the descriptors, but they can still grow very large in some cases. If
485 you receive an error message saying that chunk memory has been exhausted in --best mode,
486 try adjusting this parameter up to dedicate more memory to the descriptors. This value
487 is not relevant for Bowtie 2. Default: 512.
488
489 -I/--minins INT The minimum insert size for valid paired-end alignments. E.g. if -I 60 is specified and
490 a paired-end alignment consists of two 20-bp alignments in the appropriate orientation
491 with a 20-bp gap between them, that alignment is considered valid (as long as -X is also
492 satisfied). A 19-bp gap would not be valid in that case. Default: 0.
493
494 -X/--maxins INT The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and
495 a paired-end alignment consists of two 20-bp alignments in the proper orientation with a
496 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied).
497 A 61-bp gap would not be valid in that case. Default: 500.
498
499
500
501 Output::
502
503 --non_directional The sequencing library was constructed in a non strand-specific manner, alignments to all four
504 bisulfite strands will be reported. Default: OFF.
505
506 (The current Illumina protocol for BS-Seq is directional, in which case the strands complementary
507 to the original strands are merely theoretical and should not exist in reality. Specifying directional
508 alignments (which is the default) will only run 2 alignment threads to the original top (OT)
509 or bottom (OB) strands in parallel and report these alignments. This is the recommended option
510 for sprand-specific libraries).
511
512 --sam-no-hd Suppress SAM header lines (starting with @). This might be useful when very large input files are
513 split up into several smaller files to run concurrently and the output files are to be merged.
514
515 --quiet Print nothing besides alignments.
516
517 --vanilla Performs bisulfite mapping with Bowtie 1 and prints the 'old' output (as in Bismark 0.5.X) instead
518 of SAM format output.
519
520 -un/--unmapped Write all reads that could not be aligned to a file in the output directory. Written reads will
521 appear as they did in the input, without any translation of quality values that may have
522 taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1
523 and _2 inserted in their filenames, i.e. _unmapped_reads_1.txt and unmapped_reads_2.txt. Reads
524 with more than one valid alignment with the same number of lowest mismatches (ambiguous mapping)
525 are also written to _unmapped_reads.txt unless the option --ambiguous is specified as well.
526
527 --ambiguous Write all reads which produce more than one valid alignment with the same number of lowest
528 mismatches or other reads that fail to align uniquely to a file in the output directory.
529 Written reads will appear as they did in the input, without any of the translation of quality
530 values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two
531 parallel files with _1 and _2 inserted in theit filenames, i.e. _ambiguous_reads_1.txt and
532 _ambiguous_reads_2.txt. These reads are not written to the file specified with --un.
533
534 -o/--output_dir DIR Write all output files into this directory. By default the output files will be written into
535 the same folder as the input file(s). If the specified folder does not exist, Bismark will attempt
536 to create it first. The path to the output folder can be either relative or absolute.
537
538 --temp_dir DIR Write temporary files to this directory instead of into the same directory as the input files. If
539 the specified folder does not exist, Bismark will attempt to create it first. The path to the
540 temporary folder can be either relative or absolute.
541
542 ------
543
544 Bowtie 2 alignment options::
545
546 -N INT Sets the number of mismatches to allowed in a seed alignment during multiseed alignment.
547 Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower)
548 but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for
549 Bowtie 1 see -n).
550
551 -L INT Sets the length of the seed substrings to align during multiseed alignment. Smaller values
552 make alignment slower but more senstive. Default: the --sensitive preset of Bowtie 2 is
553 used by default, which sets -L to 20. This option is only available for Bowtie 2 (for
554 Bowtie 1 see -l).
555
556 --ignore-quals When calculating a mismatch penalty, always consider the quality value at the mismatched
557 position to be the highest possible, regardless of the actual value. I.e. input is treated
558 as though all quality values are high. This is also the default behavior when the input
559 doesn't specify quality values (e.g. in -f mode). This option is invariable and on by default.
560
561
562 Bowtie 2 paired-end options::
563
564 --no-mixed This option disables Bowtie 2's behavior to try to find alignments for the individual mates if
565 it cannot find a concordant or discordant alignment for a pair. This option is invariable and
566 and on by default.
567
568 --no-discordant Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments.
569 A discordant alignment is an alignment where both mates align uniquely, but that does not
570 satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior
571 and it is on by default.
572
573
574 Bowtie 2 effort options::
575
576 -D INT Up to INT consecutive seed extension attempts can "fail" before Bowtie 2 moves on, using
577 the alignments found so far. A seed extension "fails" if it does not yield a new best or a
578 new second-best alignment. Default: 15.
579
580 -R INT INT is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds.
581 When "re-seeding," Bowtie 2 simply chooses a new set of reads (same length, same number of
582 mismatches allowed) at different offsets and searches for more alignments. A read is considered
583 to have repetitive seeds if the total number of seed hits divided by the number of seeds
584 that aligned at least once is greater than 300. Default: 2.
585
586
587 Bowtie 2 Scoring options::
588
589 --score_min "func" Sets a function governing the minimum alignment score needed for an alignment to be considered
590 "valid" (i.e. good enough to report). This is a function of read length. For instance, specifying
591 L,0,-0.2 sets the minimum-score function f to f(x) = 0 + -0.2 * x, where x is the read length.
592 See also: setting function options at http://bowtie-bio.sourceforge.net/bowtie2. The default is
593 L,0,-0.2.
594
595
596 Bowtie 2 Reporting options::
597
598 --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
599 deprecated. It will be removed in subsequent versions. What used to be called -M mode is still the
600 default mode, but adjusting the -M setting is deprecated. Use the -D and -R options to adjust the
601 effort expended to find valid alignments.
602
603 For reference, this used to be the old (now deprecated) description of -M:
604 Bowtie 2 searches for at most INT+1 distinct, valid alignments for each read. The search terminates when it
605 can't find more distinct valid alignments, or when it finds INT+1 distinct alignments, whichever
606 happens first. Only the best alignment is reported. Information from the other alignments is used to
607 estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. Increasing -M makes
608 Bowtie 2 slower, but increases the likelihood that it will pick the correct alignment for a read that
609 aligns many places. For reads that have more than INT+1 distinct, valid alignments, Bowtie 2 does not
610 guarantee that the alignment reported is the best possible in terms of alignment score. -M is
611 always used and its default value is set to 10.
612
613 </help>
614 </tool>