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PROGRAM:

NAME

bowtie - ultrafast memory-efficient short read aligner

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 lgw01-11 Thu Nov 26 11:11:48 UTC 2015 Compiler: gcc version 5.2.1 20151123
(Ubuntu 5.2.1-25ubuntu1) Options: -O3 -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro Sizeof {int, long,
long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

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