BOWTIE(1) User Commands BOWTIE(1)
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)
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 wr-linux02 Tue Apr 24 11:37:12 UTC 2012 Compiler: gcc version 4.6.3 (Debian 4.6.3-4) Options: -O3 -Wl,--hash-style=both
-D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -O2
-fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wl,-z,relro Sizeof {int, long, long long,
void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
bowtie version 0.12.7 April 2012 BOWTIE(1)