OnWorks favicon

bowtie2 - Online in the Cloud

Run bowtie2 in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command bowtie2 that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



bowtie2 - wrapper for bowtie2-align-*


Bowtie 2 version 2.2.6 by Ben Langmead ([email protected], www.cs.jhu.edu/~langmea)


bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]

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)

-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)

qualities are Phred+33 (default)

qualities are Phred+64

qualities encoded as space-delimited integers

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

-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)

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)

do not allow 1 mismatch alignments before attempting to scan for the optimal seeded

entire read must align; no clipping (on)


local alignment; ends might be soft clipped (off)

--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)

look for multiple alignments, report best, with MAPQ


-k <int>
report up to <int> alns per read; MAPQ not meaningful


report all alignments; very slow, MAPQ not meaningful

-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)


-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)

suppress unpaired alignments for paired reads

suppress discordant alignments for paired reads

not concordant when mates extend past each other

not concordant when one mate alignment contains other

not concordant when mates overlap at all

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 supppress SAM records for unaligned reads
--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.

put '*' in SEQ and QUAL fields for secondary alignments.

-p/--threads <int> number of alignment threads to launch (1)

force SAM output order to match order of input reads

--mm use memory-mapped I/O for index; many 'bowtie's can share

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

print version information and quit

print this usage message

Use bowtie2 online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

Linux commands