DESCRIPTION

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

<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)

Input:

-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)

--large-index

force usage of a 'large' index, even if a small one is present

Alignment:

-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)

Reporting:

-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)

Output:

-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 refXXXXX.map, 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)

Colorspace:

--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

SAM:

-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

Performance:

-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

Other:

--seed <int>

seed for random number generator

--verbose

verbose output (for debugging)

--version

print version information and quit

-h/--help

print this usage message

64-bit Built on Debian-reproducible Wed, 25 May 2016 22:25:27 +0000 Compiler: gcc version 5.3.1 20160519 Options: -O3 -Wl,--hash-style=both -Wdate-time -D_FORTIFY_SOURCE=,2/ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=,format-security/ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=,format-security/ -fPIE -pie -Wl,-z,relro -Wl,-z,now Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}