Bowtie2-Teaching

Category

Bioinformatics

Program On

Teaching

Version

2.2.3

Author / Distributor

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 Bowtie2

Running Program

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

ml Bowtie2/2.2.3-foss-2016b 

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

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

cd $SLURM_SUBMIT_DIR
ml Bowtie2/2.2.3-foss-2016b
bowtie2 [options]

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, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml Bowtie2/2.2.3-foss-2016b 
bowtie2 -h
Bowtie 2 version 2.2.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage: 
  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-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).
  <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)
  --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
  -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)
  --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
  --no-dovetail      not 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

 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-head          supppress header lines, i.e. lines starting with @
  --no-sq            supppress @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.

 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

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Installation

Source code is obtained from Bowtie2

System

64-bit Linux