There is a bug in the changes we made to a part of our batch software during the downtime. The bug is affecting some users when they submit jobs to our system.


"Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. It aligns 35-base-pair reads to the human genome at a rate of 25 million reads per hour on a typical workstation. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: for the human genome, the index is typically about 2.2 GB (for unpaired alignment) or 2.9 GB (for paired-end or colorspace alignment). Multiple processors can be used simultaneously to achieve greater alignment speed. Bowtie can also output alignments in the standard SAM format, allowing Bowtie to interoperate with other tools supporting SAM, including the SAMtools consensus, SNP, and indel callers. Bowtie runs on the command line." (

Availability & Restrictions

Bowtie is available to all OSC users without restriction.

The following version of Bowtie are available on OSC systems:

Version Glenn Oakley
0.12.7 X  



To configure your environment for using PAUP, run the following command:

module load paup

Using Bowtie

On the Glenn Cluster bowtie is accessed by executing the following commands:

module load biosoftw
module load bowtie

bowtie will be added to the users PATH and can then be run with the command:

bowtie [options]* <ebwt> {-1 <m1> -2 <m2 | --12 <r> | <s>} [<hit]

Below are definitions for some of the main optional arguments:

<m1>    Comma-separated list of files containing upstream mates (or the sequences themselves, if -c is set) paired with mates in <m2>
<m2>    Comma-separated list of files containing downstream mates (or the sequences themselves if -c is set) paired with mates in <m1>
<r>     Comma-separated list of files containing Crossbow-style reads.  Can be a mixture of paired and unpaired.  Specify "-" for stdin.
<s>     Comma-separated list of files containing unpaired reads, or the sequences themselves, if -c is set.  Specify "-" for stdin.
<hit>   File to write hits to (default: stdout)



-q                       query input files are FASTQ .fq/.fastq (default)
-f                       query input files are (multi-)FASTA .fa/.mfa
-r                       query input files are raw one-sequence-per-line
-c                       query sequences given on cmd line (as <mates>, <singles>)
-C                       reads and index are in colorspace
-Q/--quals <file>        QV file(s) corresponding to CSFASTA inputs; use with -f -C
--Q1/--Q2 <file>         same as -Q, but for mate files 1 and 2 respectively
-s/--skip <int>          skip the first <int> reads/pairs in the input
-u/--qupto <int>         stop after first <int> reads/pairs (excl. skipped reads)
-5/--trim5 <int>         trim <int> bases from 5' (left) end of reads
-3/--trim3 <int>         trim <int> bases from 3' (right) end of reads
--phred33-quals          input quals are Phred+33 (default)
--phred64-quals          input quals are Phred+64 (same as --solexa1.3-quals)
--solexa-quals           input quals are from GA Pipeline ver. < 1.3
--solexa1.3-quals        input quals are from GA Pipeline ver. >= 1.3
--integer-quals          qualities are given as space-separated integers (not ASCII)


-v <int>                 report end-to-end hits w/ <=v mismatches; ignore qualities or
-n/--seedmms <int>       max mismatches in seed (can be 0-3, default: -n 2)
-e/--maqerr <int>        max sum of mismatch quals across alignment for -n (def: 70)
-l/--seedlen <int>       seed length for -n (default: 28)
--nomaqround             disable Maq-like quality rounding for -n (nearest 10 <= 30)
-I/--minins <int>        minimum insert size for paired-end alignment (default: 0)
-X/--maxins <int>        maximum insert size for paired-end alignment (default: 250)
--fr/--rf/--ff           -1, -2 mates align fw/rev, rev/fw, fw/fw (default: --fr)
--nofw/--norc            do not align to forward/reverse-complement reference strand
--maxbts <int>           max # backtracks for -n 2/3 (default: 125, 800 for --best)
--pairtries <int>        max # attempts to find mate for anchor hit (default: 100)
-y/--tryhard             try hard to find valid alignments, at the expense of speed
--chunkmbs <int>         max megabytes of RAM for best-first search frames (def: 64)


-k <int>                 report up to <int> good alignments per read (default: 1)
-a/--all                 report all alignments per read (much slower than low -k)
-m <int>                 suppress all alignments if > <int> exist (def: no limit)
-M <int>                 like -m, but reports 1 random hit (MAPQ=0); requires --best
--best                   hits guaranteed best stratum; ties broken by quality
--strata                 hits in sub-optimal strata aren't reported (requires --best)


-t/--time                print wall-clock time taken by search phases
-B/--offbase <int>       leftmost ref offset = <int> in bowtie output (default: 0)
--quiet                  print nothing but the alignments
--refout                 write alignments to files, 1 map per reference
--refidx                 refer to ref. seqs by 0-based index rather than name
--al <fname>             write aligned reads/pairs to file(s) <fname>
--un <fname>             write unaligned reads/pairs to file(s) <fname>
--max <fname>            write reads/pairs over -m limit to file(s) <fname>
--suppress <cols>        suppresses given columns (comma-delim'ed) in default output
--fullref                write entire ref name (default: only up to 1st space)


--snpphred <int>         Phred penalty for SNP when decoding colorspace (def: 30) or
--snpfrac <dec>          approx. fraction of SNP bases (e.g. 0.001); sets --snpphred
--col-cseq               print aligned colorspace seqs as colors, not decoded bases
--col-cqual              print original colorspace quals, not decoded quals
--col-keepends           keep nucleotides at extreme ends of decoded alignment


-S/--sam                 write hits in SAM format
--mapq <int>             default mapping quality (MAPQ) to print for SAM alignments
--sam-nohead             supppress header lines (starting with @) for SAM output
--sam-nosq               supppress @SQ header lines for SAM output
--sam-RG <text>          add <text> (usually "lab=value") to @RG line of SAM header


-o/--offrate <int>       override offrate of index; must be >= index's offrate
-p/--threads <int>       number of alignment threads to launch (default: 1)
--mm                     use memory-mapped I/O for index; many 'bowtie's can share
--shmem                  use shared mem for index; many 'bowtie's can share


--seed <int>             seed for random number generator
--verbose                verbose output (for debugging)
--version                print version information and quit
-h/--help                print this usage message


Batch Usage

The following is an example batch script file.

#PBS -n bowtie_test
#PBS -l walltime=00:05:00
#PBS -l nodes=1:ppn=4

module load biosoftw
module load bowtie-0.12.7
cp /usr/local/biosoftw/bowtie-$BOWTIE_VERSION/genomes/NC_008253.fna .
bowtie-build NC_008253.fna e_coli
bowtie –p 4 e_coli -c ATGCATCATGCGCCAT


The following scripts fail due to an ftp error:,, and  The following scripts fail to obtain all of the fasta format files prior to bowtie conversion and fail:,,,,,  The follow script does not work properly on the Glenn Cluster:

Further Reading

Fields of Science: