Shtsai at 00:14, 5 April 2026

2026-04-05T00:14:02Z

← Older revision		Revision as of 20:14, 4 April 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

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

	Sapelo2		Sapelo2

	=== 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 14:32, 8 July 2025

2025-07-08T14:32:06Z

← Older revision		Revision as of 10:32, 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 class="gscript">		<pre class="gscript">
	ml Bowtie2/2.5.2-GCC-11.3.0		ml Bowtie2/2.5.2-GCC-11.3.0
			</pre>

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

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	</pre>		</pre>

	~~To use version 2.4.4, please load the module with~~
	~~<pre class="gscript">~~
	~~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>~~

	Here is an example of a shell script, sub.sh, to run on the batch queue:		Here is an example of a shell script, sub.sh, to run on the batch queue:

Shtsai at 17:54, 12 June 2024

2024-06-12T17:54:10Z

← Older revision		Revision as of 13:54, 12 June 2024
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	[[Category:~~Teaching~~]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		=== Category ===

Chelsea: /* Running Program */

2024-05-14T15:37:21Z

Running Program

← Older revision		Revision as of 11:37, 14 May 2024
Line 63:		Line 63:
	In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.		In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

	Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application \| Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session \| Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Chelsea: Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.4.1, 2.4.4, 2.4.5, 2.5.2 === Author / Distributor === [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2] === 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..."

2024-05-14T15:36:46Z

Created page with "Category:Teaching Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.4.1, 2.4.4, 2.4.5, 2.5.2 === Author / Distributor === [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2] === 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..."

New page

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===
2.4.1, 2.4.4, 2.4.5, 2.5.2

=== Author / Distributor ===

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

=== 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."
More details are at [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

=== Running Program ===

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
<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">
ml Bowtie2/2.4.5-GCC-11.3.0
</pre>

To use version 2.4.4, please load the module with
<pre class="gscript">
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>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_Bowtie2 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=Bowtie2.%j.out 
<nowiki>#</nowiki>SBATCH --error=Bowtie2.%j.err 

cd $SLURM_SUBMIT_DIR 
ml Bowtie2/2.4.5-GCC-11.3.0 
bowtie2 [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml Bowtie2/2.4.5-GCC-11.3.0
bowtie2 -h

Bowtie 2 version 2.4.5 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved | -b <bam>} [-S <sam>]

<bt2-idx> Index filename prefix (minus trailing .X.bt2).
NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
<m1> Files with #1 mates, paired with files in <m2>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<m2> Files with #2 mates, paired with files in <m1>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<r> Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
 Files with interleaved paired-end FASTQ/FASTA reads
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)

<m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

Input:
-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
-f query input files are (multi-)FASTA .fa/.mfa
-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
-s/--skip <int> skip the first <int> reads/pairs in the input (none)
-u/--upto <int> stop after first <int> reads/pairs (no limit)
-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)
--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)
--phred64 qualities are Phred+64
--int-quals qualities encoded as space-delimited integers

Presets: Same as:
For --end-to-end:
--very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
--fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
--sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
--very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

For --local:
--very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
--fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
--sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
--very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

Alignment:
-N <int> max # mismatches in seed alignment; can be 0 or 1 (0)
-L <int> length of seed substrings; must be >3, <32 (22)
-i <func> interval between seed substrings w/r/t read len (S,1,1.15)
--n-ceil <func> func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
--dpad <int> include <int> extra ref chars on sides of DP table (15)
--gbar <int> disallow gaps within <int> nucs of read extremes (4)
--ignore-quals treat all quality values as 30 on Phred scale (off)
--nofw do not align forward (original) version of read (off)
--norc do not align reverse-complement version of read (off)
--no-1mm-upfront do not allow 1 mismatch alignments before attempting to
scan for the optimal seeded alignments
--end-to-end entire read must align; no clipping (on)
OR
--local local alignment; ends might be soft clipped (off)

Scoring:
--ma <int> match bonus (0 for --end-to-end, 2 for --local)
--mp <int> max penalty for mismatch; lower qual = lower penalty (6)
--np <int> penalty for non-A/C/G/Ts in read/ref (1)
--rdg <int>,<int> read gap open, extend penalties (5,3)
--rfg <int>,<int> reference gap open, extend penalties (5,3)
--score-min <func> min acceptable alignment score w/r/t read length
(G,20,8 for local, L,-0.6,-0.6 for end-to-end)

Reporting:
(default) look for multiple alignments, report best, with MAPQ
OR
-k <int> report up to <int> alns per read; MAPQ not meaningful
OR
-a/--all report all alignments; very slow, MAPQ not meaningful

Effort:
-D <int> give up extending after <int> failed extends in a row (15)
-R <int> for reads w/ repetitive seeds, try <int> sets of seeds (2)

Paired-end:
-I/--minins <int> minimum fragment length (0)
-X/--maxins <int> maximum fragment length (500)
--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
--no-mixed suppress unpaired alignments for paired reads
--no-discordant suppress discordant alignments for paired reads
--dovetail concordant when mates extend past each other
--no-contain not concordant when one mate alignment contains other
--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:
-t/--time print wall-clock time taken by search phases
--un <path> write unpaired reads that didn't align 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>
--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.
--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
--quiet print nothing to stderr except serious errors
--met-file <path> send metrics to file at <path> (off)
--met-stderr send metrics to stderr (off)
--met <int> report internal counters & metrics every <int> secs (1)
--no-unal suppress SAM records for unaligned reads
--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 <text> add <text> ("lab:value") to @RG line of SAM header.
Note: @RG line only printed when --rg-id is set.
--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
--sam-append-comment
Append FASTA/FASTQ comment to SAM record

Performance:
-p/--threads <int> number of alignment threads to launch (1)
--reorder force SAM output order to match order of input reads
--mm use memory-mapped I/O for index; many 'bowtie's can share

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

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

=== Installation ===

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

=== System ===
64-bit Linux

Bowtie2-Sapelo2 - Revision history

Shtsai at 00:14, 5 April 2026

Chelsea at 14:32, 8 July 2025

Shtsai at 17:54, 12 June 2024

Chelsea: /* Running Program */