Bowtie2-Teaching - Revision history

Shtsai at 00:14, 5 April 2026

2026-04-05T00:14:51Z

← Older revision		Revision as of 20:14, 4 April 2026
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	[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Teaching		Teaching

	=== Version ===		== Version ==
	2.4.5, 2.5.1, 2.5.2		2.4.5, 2.5.1, 2.5.2

	=== Author / Distributor ===		== Author / Distributor ==

	[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]		[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

	=== Description ===		== Description ==
	"Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."		"Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."
	More details are at [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]		More details are at [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

	=== Running Program ===		== Running Program ==

	The last version of this application is at /apps/eb/Bowtie2/2.5.2-GCC-11.3.0		The last version of this application is at /apps/eb/Bowtie2/2.5.2-GCC-11.3.0
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==

	<pre class="gcommand">		<pre class="gcommand">
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	Source code is obtained from [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]		Source code is obtained from [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Chelsea at 14:34, 8 July 2025

2025-07-08T14:34:15Z

← Older revision		Revision as of 10:34, 8 July 2025
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	=== Version ===		=== Version ===
	2.4.1, 2.4.~~4, 2.4.5~~, 2.5.2		2.4.5, 2.5.1, 2.5.2

	=== Author / Distributor ===		=== Author / Distributor ===
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	</pre>		</pre>

	To use version 2.4.5, please load the module with		To use version 2.5.1, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Bowtie2/2.4.5-GCC-11.3.0		ml Bowtie2/2.5.1-GCC-12.3.0
	</pre>		</pre>

	To use version 2.4.4, please load the module with		To use version 2.4.5, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Bowtie2/2.4.4-GCC-11~~.2.0~~		ml Bowtie2/2.4.5-GCC-11.3.0
	~~</pre>~~

	~~To use version 2.4.1, please load the module with~~
	~~<pre class="gscript">~~
	~~ml Bowtie2/2.4.1-GCC-8~~.3.0
	</pre>		</pre>

Chelsea: /* Version */

2024-05-09T14:12:11Z

Version

← Older revision		Revision as of 10:12, 9 May 2024
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	=== Version ===		=== Version ===
	2.4.1, 2.4.4, 2.4.5		2.4.1, 2.4.4, 2.4.5, 2.5.2

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	The last version of this application is at /apps/eb/Bowtie2/2.4.5-GCC-11.3.0		The last version of this application is at /apps/eb/Bowtie2/2.5.2-GCC-11.3.0

	To use this version, please load the module with		To use this version, please load the module with
			<pre class="gscript">
			ml Bowtie2/2.5.2-GCC-11.3.0
			</pre>

			To use version 2.4.5, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Bowtie2/2.4.5-GCC-11.3.0		ml Bowtie2/2.4.5-GCC-11.3.0

Shtsai at 15:59, 5 September 2023

2023-09-05T15:59:07Z

← Older revision		Revision as of 11:59, 5 September 2023
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	=== Version ===		=== Version ===
	2.3.5.1, 2.4.1		2.4.1, 2.4.4, 2.4.5

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	The last version of this application is at /apps/eb/Bowtie2/2.4.1-GCC-8.3.0		The last version of this application is at /apps/eb/Bowtie2/2.4.5-GCC-11.3.0

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Bowtie2/2.4.1-GCC-8.3.0		ml Bowtie2/2.4.5-GCC-11.3.0
	</pre>		</pre>

	To use version 2.3.~~5.1~~, please load the module with		To use version 2.4.4, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Bowtie2/2.3.5.1-GCC-8.3.0		ml Bowtie2/2.4.4-GCC-11.2.0
			</pre>

			To use version 2.4.1, please load the module with
			<pre class="gscript">
			ml Bowtie2/2.4.1-GCC-8.3.0
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml Bowtie2/2.4.1-GCC-8.3.0<br>		ml Bowtie2/2.4.5-GCC-11.3.0<br>
	bowtie2 <u>[options]</u><br>		bowtie2 <u>[options]</u><br>
	</div>		</div>
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	<pre class="gcommand">		<pre class="gcommand">
	ml Bowtie2/2.4.1-GCC-8.3.0		ml Bowtie2/2.4.5-GCC-11.3.0
	bowtie2 -h		bowtie2 -h

	Bowtie 2 version 2.4.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)		Bowtie 2 version 2.4.5 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
	Usage:		Usage:
	bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> \| -U <r> \| --interleaved <i> \| -b <bam>} [-S <sam>]		bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> \| -U <r> \| --interleaved <i> \| -b <bam>} [-S <sam>]
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	BAM:		BAM:
	--align-paired-reads Bowtie2 will, by default, attempt to align unpaired BAM reads.		--align-paired-reads
			Bowtie2 will, by default, attempt to align unpaired BAM reads.
	Use this option to align paired-end reads instead.		Use this option to align paired-end reads instead.
	--preserve-tags Preserve tags from the original BAM record by		--preserve-tags Preserve tags from the original BAM record by
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	Note: @RG line only printed when --rg-id is set.		Note: @RG line only printed when --rg-id is set.
	--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.		--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.
	--sam-no-qname-trunc Suppress standard behavior of truncating readname at first whitespace		--sam-no-qname-trunc
	at the expense of generating non-standard SAM.		Suppress standard behavior of truncating readname at first whitespace
			at the expense of generating non-standard SAM.
	--xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.		--xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
	--soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN		--soft-clipped-unmapped-tlen
			Exclude soft-clipped bases when reporting TLEN
			--sam-append-comment
			Append FASTA/FASTQ comment to SAM record

	Performance:		Performance:
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	--qc-filter filter out reads that are bad according to QSEQ filter		--qc-filter filter out reads that are bad according to QSEQ filter
	--seed <int> seed for random number generator (0)		--seed <int> seed for random number generator (0)
	--non-deterministic seed rand. gen. arbitrarily instead of using read attributes		--non-deterministic
			seed rand. gen. arbitrarily instead of using read attributes
	--version print version information and quit		--version print version information and quit
	-h/--help print this usage message		-h/--help print this usage message

	</pre>		</pre>
	[[#top\|Back to Top]]		[[#top\|Back to Top]]

Shtsai at 17:26, 27 August 2020

2020-08-27T17:26:09Z

← Older revision		Revision as of 13:26, 27 August 2020
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	=== Version ===		=== Version ===
	2.3.4.1		2.3.5.1, 2.4.1

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	The last version of this application is at ~~/usr/local~~/apps/eb/Bowtie2/2.3.4.1-~~foss~~-~~2016b~~		The last version of this application is at /apps/eb/Bowtie2/2.4.1-GCC-8.3.0

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Bowtie2/2.3.4.1-~~foss~~-~~2016b~~		ml Bowtie2/2.4.1-GCC-8.3.0
			</pre>

			To use version 2.3.5.1, please load the module with
			<pre class="gscript">
			ml Bowtie2/2.3.5.1-GCC-8.3.0
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml Bowtie2/2.3.4.1-~~foss~~-~~2016b~~<br>		ml Bowtie2/2.4.1-GCC-8.3.0<br>
	bowtie2 <u>[options]</u><br>		bowtie2 <u>[options]</u><br>
	</div>		</div>
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	<pre class="gcommand">		<pre class="gcommand">
	ml Bowtie2/2.3.4.1-~~foss~~-~~2016b~~		ml Bowtie2/2.4.1-GCC-8.3.0
	bowtie2 -h		bowtie2 -h
	Bowtie 2 version 2.3.4.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
			Bowtie 2 version 2.4.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
	Usage:		Usage:
	bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> \| -U <r> \| --interleaved <i>} [-S <sam>]		bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> \| -U <r> \| --interleaved <i> \| -b <bam>} [-S <sam>]

	<bt2-idx> Index filename prefix (minus trailing .X.bt2).		<bt2-idx> Index filename prefix (minus trailing .X.bt2).
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	<r> Files with unpaired reads.		<r> Files with unpaired reads.
	Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).		Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
	<i> Files with interleaved paired-end FASTQ reads		<i> Files with interleaved paired-end FASTQ/FASTA reads
	Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).		Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
			<bam> Files are unaligned BAM sorted by read name.
	<sam> File for SAM output (default: stdout)		<sam> File for SAM output (default: stdout)

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	-5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)		-5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)
	-3/--trim3 <int> trim <int> bases from 3'/right end of reads (0)		-3/--trim3 <int> trim <int> bases from 3'/right end of reads (0)
			--trim-to [3:\|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end
			If the read end is not specified then it defaults to 3 (0)
	--phred33 qualities are Phred+33 (default)		--phred33 qualities are Phred+33 (default)
	--phred64 qualities are Phred+64		--phred64 qualities are Phred+64
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	--no-contain not concordant when one mate alignment contains other		--no-contain not concordant when one mate alignment contains other
	--no-overlap not concordant when mates overlap at all		--no-overlap not concordant when mates overlap at all

			BAM:
			--align-paired-reads Bowtie2 will, by default, attempt to align unpaired BAM reads.
			Use this option to align paired-end reads instead.
			--preserve-tags Preserve tags from the original BAM record by
			appending them to the end of the corresponding SAM output.

	Output:		Output:
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	--version print version information and quit		--version print version information and quit
	-h/--help print this usage message		-h/--help print this usage message

	</pre>		</pre>
	[[#top\|Back to Top]]		[[#top\|Back to Top]]

Yhuang at 19:44, 15 August 2018

2018-08-15T19:44:21Z

← Older revision		Revision as of 15:44, 15 August 2018
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	=== Version ===		=== Version ===
	2.3.3		2.3.4.1

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Description ===		=== Description ===
	"Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."		"Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."
	More details are at [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]		More details are at [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

	=== Running Program ===		=== Running Program ===

	The last version of this application is at /usr/local/apps/eb/Bowtie2/2.3.3-foss-2016b		The last version of this application is at /usr/local/apps/eb/Bowtie2/2.3.4.1-foss-2016b

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Bowtie2/2.3.3-foss-2016b		ml Bowtie2/2.3.4.1-foss-2016b
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml Bowtie2/2.3.3-foss-2016b<br>		ml Bowtie2/2.3.4.1-foss-2016b<br>
	bowtie2 <u>[options]</u><br>		bowtie2 <u>[options]</u><br>
	</div>		</div>
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	<pre class="gcommand">		<pre class="gcommand">
	ml Bowtie2/2.3.3-foss-2016b		ml Bowtie2/2.3.4.1-foss-2016b
	bowtie2 -h		bowtie2 -h
	Bowtie 2 version 2.3.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)		Bowtie 2 version 2.3.4.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
	Usage:		Usage:
	bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> \| -U <r> \| --interleaved <i>} [-S <sam>]		bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> \| -U <r> \| --interleaved <i>} [-S <sam>]
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	-f query input files are (multi-)FASTA .fa/.mfa		-f query input files are (multi-)FASTA .fa/.mfa
	-r query input files are raw one-sequence-per-line		-r query input files are raw one-sequence-per-line
			-F k:<int>,i:<int> query input files are continuous FASTA where reads
			are substrings (k-mers) extracted from a FASTA file <s>
			and aligned at offsets 1, 1+i, 1+2i ... end of reference
	-c <m1>, <m2>, <r> are sequences themselves, not files		-c <m1>, <m2>, <r> are sequences themselves, not files
	-s/--skip <int> skip the first <int> reads/pairs in the input (none)		-s/--skip <int> skip the first <int> reads/pairs in the input (none)
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	Output:		Output:
	-t/--time print wall-clock time taken by search phases		-t/--time print wall-clock time taken by search phases
	--un <path> write unpaired reads that didn't align to <path>		--un <path> write unpaired reads that didn't align to <path>
	--al <path> write unpaired reads that aligned at least once to <path>		--al <path> write unpaired reads that aligned at least once to <path>
	--un-conc <path> write pairs that didn't align concordantly to <path>		--un-conc <path> write pairs that didn't align concordantly to <path>
	--al-conc <path> write pairs that aligned concordantly at least once to <path>		--al-conc <path> write pairs that aligned concordantly at least once to <path>
	(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.		(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
	--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)		--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
	--quiet print nothing to stderr except serious errors		--quiet print nothing to stderr except serious errors
	--met-file <path> send metrics to file at <path> (off)		--met-file <path> send metrics to file at <path> (off)
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	Note: @RG line only printed when --rg-id is set.		Note: @RG line only printed when --rg-id is set.
	--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.		--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.
	--sam-~~noqname~~-trunc Suppress standard behavior of truncating readname at first whitespace		--sam-no-qname-trunc Suppress standard behavior of truncating readname at first whitespace
	at the expense of generating non-standard SAM.		at the expense of generating non-standard SAM.
	--xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.		--xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.

Yhuang at 19:44, 15 August 2018

2018-08-15T19:44:14Z

← Older revision		Revision as of 15:44, 15 August 2018
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	=== Version ===		=== Version ===
	2.2.3		2.3.3

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	The last version of this application is at /usr/local/apps/eb/Bowtie2/2.2.3-foss-2016b		The last version of this application is at /usr/local/apps/eb/Bowtie2/2.3.3-foss-2016b

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Bowtie2/2.2.3-foss-2016b		ml Bowtie2/2.3.3-foss-2016b
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml Bowtie2/2.2.3-foss-2016b<br>		ml Bowtie2/2.3.3-foss-2016b<br>
	bowtie2 <u>[options]</u><br>		bowtie2 <u>[options]</u><br>
	</div>		</div>
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	<pre class="gcommand">		<pre class="gcommand">
	ml Bowtie2/2.2.3-foss-2016b		ml Bowtie2/2.3.3-foss-2016b
	bowtie2 -h		bowtie2 -h
	Bowtie 2 version 2.2.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)		Bowtie 2 version 2.3.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
	Usage:		Usage:
	bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> \| -U <r>} [-S <sam>]		bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> \| -U <r> \| --interleaved <i>} [-S <sam>]

	<bt2-idx> Index filename prefix (minus trailing .X.bt2).		<bt2-idx> Index filename prefix (minus trailing .X.bt2).
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	Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).		Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
	<r> Files with unpaired reads.		<r> Files with unpaired reads.
			Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
			<i> Files with interleaved paired-end FASTQ reads
	Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).		Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
	<sam> File for SAM output (default: stdout)		<sam> File for SAM output (default: stdout)
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	Input:		Input:
	-q query input files are FASTQ .fq/.fastq (default)		-q query input files are FASTQ .fq/.fastq (default)
			--tab5 query input files are TAB5 .tab5
			--tab6 query input files are TAB6 .tab6
	--qseq query input files are in Illumina's qseq format		--qseq query input files are in Illumina's qseq format
	-f query input files are (multi-)FASTA .fa/.mfa		-f query input files are (multi-)FASTA .fa/.mfa
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	--no-mixed suppress unpaired alignments for paired reads		--no-mixed suppress unpaired alignments for paired reads
	--no-discordant suppress discordant alignments for paired reads		--no-discordant suppress discordant alignments for paired reads
	-~~-no~~-dovetail ~~not~~ concordant when mates extend past each other		--dovetail concordant when mates extend past each other
	--no-contain not concordant when one mate alignment contains other		--no-contain not concordant when one mate alignment contains other
	--no-overlap not concordant when mates overlap at all		--no-overlap not concordant when mates overlap at all
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	--met-stderr send metrics to stderr (off)		--met-stderr send metrics to stderr (off)
	--met <int> report internal counters & metrics every <int> secs (1)		--met <int> report internal counters & metrics every <int> secs (1)
	--no-head ~~supppress~~ header lines, i.e. lines starting with @		--no-unal suppress SAM records for unaligned reads
	--no-sq ~~supppress~~ @SQ header lines		--no-head suppress header lines, i.e. lines starting with @
			--no-sq suppress @SQ header lines
	--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field		--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field
	--rg <text> add <text> ("lab:value") to @RG line of SAM header.		--rg <text> add <text> ("lab:value") to @RG line of SAM header.
	Note: @RG line only printed when --rg-id is set.		Note: @RG line only printed when --rg-id is set.
	--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.		--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.
			--sam-noqname-trunc Suppress standard behavior of truncating readname at first whitespace
			at the expense of generating non-standard SAM.
			--xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
			--soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN

	Performance:		Performance:

Yhuang at 19:44, 15 August 2018

2018-08-15T19:44:07Z

← Older revision		Revision as of 15:44, 15 August 2018
Line 9:		Line 9:

	=== Version ===		=== Version ===
	2.3~~.4.1~~		2.2.3

	=== Author / Distributor ===		=== Author / Distributor ===
Line 16:		Line 16:

	=== Description ===		=== Description ===
	"Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."		"Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."
	More details are at [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]		More details are at [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

	=== Running Program ===		=== Running Program ===

	The last version of this application is at /usr/local/apps/eb/Bowtie2/2.3~~.4.1~~-foss-2016b		The last version of this application is at /usr/local/apps/eb/Bowtie2/2.2.3-foss-2016b

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Bowtie2/2.3~~.4.1~~-foss-2016b		ml Bowtie2/2.2.3-foss-2016b
	</pre>		</pre>

Line 43:		Line 43:

	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml Bowtie2/2.3~~.4.1~~-foss-2016b<br>		ml Bowtie2/2.2.3-foss-2016b<br>
	bowtie2 <u>[options]</u><br>		bowtie2 <u>[options]</u><br>
	</div>		</div>
Line 59:		Line 59:

	<pre class="gcommand">		<pre class="gcommand">
	ml Bowtie2/2.3~~.4.1~~-foss-2016b		ml Bowtie2/2.2.3-foss-2016b
	bowtie2 -h		bowtie2 -h
	Bowtie 2 version 2.3~~.4.1~~ by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)		Bowtie 2 version 2.2.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
	Usage:		Usage:
	bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> \| -U <r~~> \| --interleaved <i~~>} [-S <sam>]		bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> \| -U <r>} [-S <sam>]

	<bt2-idx> Index filename prefix (minus trailing .X.bt2).		<bt2-idx> Index filename prefix (minus trailing .X.bt2).
Line 72:		Line 72:
	Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).		Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
	<r> Files with unpaired reads.		<r> Files with unpaired reads.
	~~Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).~~
	~~<i> Files with interleaved paired-end FASTQ reads~~
	Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).		Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
	<sam> File for SAM output (default: stdout)		<sam> File for SAM output (default: stdout)
Line 84:		Line 82:
	Input:		Input:
	-q query input files are FASTQ .fq/.fastq (default)		-q query input files are FASTQ .fq/.fastq (default)
	~~--tab5 query input files are TAB5 .tab5~~
	~~--tab6 query input files are TAB6 .tab6~~
	--qseq query input files are in Illumina's qseq format		--qseq query input files are in Illumina's qseq format
	-f query input files are (multi-)FASTA .fa/.mfa		-f query input files are (multi-)FASTA .fa/.mfa
	-r query input files are raw one-sequence-per-line		-r query input files are raw one-sequence-per-line
	~~-F k:<int>,i:<int> query input files are continuous FASTA where reads~~
	~~are substrings (k-mers) extracted from a FASTA file <s>~~
	~~and aligned at offsets 1, 1+i, 1+2i ... end of reference~~
	-c <m1>, <m2>, <r> are sequences themselves, not files		-c <m1>, <m2>, <r> are sequences themselves, not files
	-s/--skip <int> skip the first <int> reads/pairs in the input (none)		-s/--skip <int> skip the first <int> reads/pairs in the input (none)
Line 156:		Line 149:
	--no-mixed suppress unpaired alignments for paired reads		--no-mixed suppress unpaired alignments for paired reads
	--no-discordant suppress discordant alignments for paired reads		--no-discordant suppress discordant alignments for paired reads
	--dovetail concordant when mates extend past each other		--no-dovetail not concordant when mates extend past each other
	--no-contain not concordant when one mate alignment contains other		--no-contain not concordant when one mate alignment contains other
	--no-overlap not concordant when mates overlap at all		--no-overlap not concordant when mates overlap at all
Line 162:		Line 155:
	Output:		Output:
	-t/--time print wall-clock time taken by search phases		-t/--time print wall-clock time taken by search phases
	--un <path> write unpaired reads that didn't align to <path>		--un <path> write unpaired reads that didn't align to <path>
	--al <path> write unpaired reads that aligned at least once to <path>		--al <path> write unpaired reads that aligned at least once to <path>
	--un-conc <path> write pairs that didn't align concordantly to <path>		--un-conc <path> write pairs that didn't align concordantly to <path>
	--al-conc <path> write pairs that aligned concordantly at least once to <path>		--al-conc <path> write pairs that aligned concordantly at least once to <path>
	(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.		(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
	--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)		--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
	--quiet print nothing to stderr except serious errors		--quiet print nothing to stderr except serious errors
	--met-file <path> send metrics to file at <path> (off)		--met-file <path> send metrics to file at <path> (off)
	--met-stderr send metrics to stderr (off)		--met-stderr send metrics to stderr (off)
	--met <int> report internal counters & metrics every <int> secs (1)		--met <int> report internal counters & metrics every <int> secs (1)
	~~--no-unal suppress SAM records for unaligned reads~~		--no-head supppress header lines, i.e. lines starting with @
	--no-head ~~suppress~~ header lines, i.e. lines starting with @		--no-sq supppress @SQ header lines
	--no-sq ~~suppress~~ @SQ header lines
	--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field		--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field
	--rg <text> add <text> ("lab:value") to @RG line of SAM header.		--rg <text> add <text> ("lab:value") to @RG line of SAM header.
	Note: @RG line only printed when --rg-id is set.		Note: @RG line only printed when --rg-id is set.
	--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.		--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.
	~~--sam-no-qname-trunc Suppress standard behavior of truncating readname at first whitespace~~
	~~at the expense of generating non-standard SAM.~~
	~~--xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.~~
	~~--soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN~~

	Performance:		Performance:

Yhuang at 19:26, 15 August 2018

2018-08-15T19:26:25Z

← Older revision		Revision as of 15:26, 15 August 2018
Line 9:		Line 9:

	=== Version ===		=== Version ===
	2.3.3		2.3.4.1

	=== Author / Distributor ===		=== Author / Distributor ===
Line 16:		Line 16:

	=== Description ===		=== Description ===
	"Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."		"Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."
	More details are at [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]		More details are at [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

	=== Running Program ===		=== Running Program ===

	The last version of this application is at /usr/local/apps/eb/Bowtie2/2.3.3-foss-2016b		The last version of this application is at /usr/local/apps/eb/Bowtie2/2.3.4.1-foss-2016b

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Bowtie2/2.3.3-foss-2016b		ml Bowtie2/2.3.4.1-foss-2016b
	</pre>		</pre>

Line 43:		Line 43:

	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml Bowtie2/2.3.3-foss-2016b<br>		ml Bowtie2/2.3.4.1-foss-2016b<br>
	bowtie2 <u>[options]</u><br>		bowtie2 <u>[options]</u><br>
	</div>		</div>
Line 59:		Line 59:

	<pre class="gcommand">		<pre class="gcommand">
	ml Bowtie2/2.3.3-foss-2016b		ml Bowtie2/2.3.4.1-foss-2016b
	bowtie2 -h		bowtie2 -h
	Bowtie 2 version 2.3.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)		Bowtie 2 version 2.3.4.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
	Usage:		Usage:
	bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> \| -U <r> \| --interleaved <i>} [-S <sam>]		bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> \| -U <r> \| --interleaved <i>} [-S <sam>]
Line 89:		Line 89:
	-f query input files are (multi-)FASTA .fa/.mfa		-f query input files are (multi-)FASTA .fa/.mfa
	-r query input files are raw one-sequence-per-line		-r query input files are raw one-sequence-per-line
			-F k:<int>,i:<int> query input files are continuous FASTA where reads
			are substrings (k-mers) extracted from a FASTA file <s>
			and aligned at offsets 1, 1+i, 1+2i ... end of reference
	-c <m1>, <m2>, <r> are sequences themselves, not files		-c <m1>, <m2>, <r> are sequences themselves, not files
	-s/--skip <int> skip the first <int> reads/pairs in the input (none)		-s/--skip <int> skip the first <int> reads/pairs in the input (none)
Line 159:		Line 162:
	Output:		Output:
	-t/--time print wall-clock time taken by search phases		-t/--time print wall-clock time taken by search phases
	--un <path> write unpaired reads that didn't align to <path>		--un <path> write unpaired reads that didn't align to <path>
	--al <path> write unpaired reads that aligned at least once to <path>		--al <path> write unpaired reads that aligned at least once to <path>
	--un-conc <path> write pairs that didn't align concordantly to <path>		--un-conc <path> write pairs that didn't align concordantly to <path>
	--al-conc <path> write pairs that aligned concordantly at least once to <path>		--al-conc <path> write pairs that aligned concordantly at least once to <path>
	(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.		(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
	--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)		--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
	--quiet print nothing to stderr except serious errors		--quiet print nothing to stderr except serious errors
	--met-file <path> send metrics to file at <path> (off)		--met-file <path> send metrics to file at <path> (off)
Line 176:		Line 179:
	Note: @RG line only printed when --rg-id is set.		Note: @RG line only printed when --rg-id is set.
	--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.		--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.
	--sam-~~noqname~~-trunc Suppress standard behavior of truncating readname at first whitespace		--sam-no-qname-trunc Suppress standard behavior of truncating readname at first whitespace
	at the expense of generating non-standard SAM.		at the expense of generating non-standard SAM.
	--xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.		--xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.

Yhuang at 19:26, 15 August 2018

2018-08-15T19:26:16Z

← Older revision		Revision as of 15:26, 15 August 2018
Line 9:		Line 9:

	=== Version ===		=== Version ===
	2.2.3		2.3.3

	=== Author / Distributor ===		=== Author / Distributor ===
Line 21:		Line 21:
	=== Running Program ===		=== Running Program ===

	The last version of this application is at /usr/local/apps/eb/Bowtie2/2.2.3-foss-2016b		The last version of this application is at /usr/local/apps/eb/Bowtie2/2.3.3-foss-2016b

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Bowtie2/2.2.3-foss-2016b		ml Bowtie2/2.3.3-foss-2016b
	</pre>		</pre>

Line 43:		Line 43:

	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml Bowtie2/2.2.3-foss-2016b<br>		ml Bowtie2/2.3.3-foss-2016b<br>
	bowtie2 <u>[options]</u><br>		bowtie2 <u>[options]</u><br>
	</div>		</div>
Line 59:		Line 59:

	<pre class="gcommand">		<pre class="gcommand">
	ml Bowtie2/2.2.3-foss-2016b		ml Bowtie2/2.3.3-foss-2016b
	bowtie2 -h		bowtie2 -h
	Bowtie 2 version 2.2.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)		Bowtie 2 version 2.3.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
	Usage:		Usage:
	bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> \| -U <r>} [-S <sam>]		bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> \| -U <r> \| --interleaved <i>} [-S <sam>]

	<bt2-idx> Index filename prefix (minus trailing .X.bt2).		<bt2-idx> Index filename prefix (minus trailing .X.bt2).
Line 72:		Line 72:
	Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).		Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
	<r> Files with unpaired reads.		<r> Files with unpaired reads.
			Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
			<i> Files with interleaved paired-end FASTQ reads
	Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).		Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
	<sam> File for SAM output (default: stdout)		<sam> File for SAM output (default: stdout)
Line 82:		Line 84:
	Input:		Input:
	-q query input files are FASTQ .fq/.fastq (default)		-q query input files are FASTQ .fq/.fastq (default)
			--tab5 query input files are TAB5 .tab5
			--tab6 query input files are TAB6 .tab6
	--qseq query input files are in Illumina's qseq format		--qseq query input files are in Illumina's qseq format
	-f query input files are (multi-)FASTA .fa/.mfa		-f query input files are (multi-)FASTA .fa/.mfa
Line 149:		Line 153:
	--no-mixed suppress unpaired alignments for paired reads		--no-mixed suppress unpaired alignments for paired reads
	--no-discordant suppress discordant alignments for paired reads		--no-discordant suppress discordant alignments for paired reads
	-~~-no~~-dovetail ~~not~~ concordant when mates extend past each other		--dovetail concordant when mates extend past each other
	--no-contain not concordant when one mate alignment contains other		--no-contain not concordant when one mate alignment contains other
	--no-overlap not concordant when mates overlap at all		--no-overlap not concordant when mates overlap at all
Line 165:		Line 169:
	--met-stderr send metrics to stderr (off)		--met-stderr send metrics to stderr (off)
	--met <int> report internal counters & metrics every <int> secs (1)		--met <int> report internal counters & metrics every <int> secs (1)
	--no-head ~~supppress~~ header lines, i.e. lines starting with @		--no-unal suppress SAM records for unaligned reads
	--no-sq ~~supppress~~ @SQ header lines		--no-head suppress header lines, i.e. lines starting with @
			--no-sq suppress @SQ header lines
	--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field		--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field
	--rg <text> add <text> ("lab:value") to @RG line of SAM header.		--rg <text> add <text> ("lab:value") to @RG line of SAM header.
	Note: @RG line only printed when --rg-id is set.		Note: @RG line only printed when --rg-id is set.
	--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.		--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.
			--sam-noqname-trunc Suppress standard behavior of truncating readname at first whitespace
			at the expense of generating non-standard SAM.
			--xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
			--soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN

	Performance:		Performance: