bowtie(1) ultrafast memory-efficient short read aligner


Usage: bowtie [options]* <ebwt> {-1 <m1> -2 <m2> | --12 <r> | <s>} [<hit>]
Comma-separated list of files containing upstream mates (or the sequences themselves, if -c is set) paired with mates in <m2>
Comma-separated list of files containing downstream mates (or the sequences themselves if -c is set) paired with mates in <m1>
Comma-separated list of files containing Crossbow-style reads. Can be a mixture of paired and unpaired. Specify "-" for stdin.
Comma-separated list of files containing unpaired reads, or the sequences themselves, if -c is set. Specify "-" for stdin.
File to write hits to (default: stdout)


query input files are FASTQ .fq/.fastq (default)
query input files are (multi-)FASTA .fa/.mfa
query input files are raw one-sequence-per-line
query sequences given on cmd line (as <mates>, <singles>)
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
input quals are Phred+33 (default)
input quals are Phred+64 (same as --solexa1.3-quals)
input quals are from GA Pipeline ver. < 1.3
input quals are from GA Pipeline ver. >= 1.3
qualities are given as space-separated integers (not ASCII)
force usage of a 'large' index, even if a small one is present


-v <int>
report end-to-end hits w/ <=v mismatches; ignore qualities
-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)
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)
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)
try hard to find valid alignments, at the expense of speed
--chunkmbs <int>
max megabytes of RAM for best-first search frames (def: 64)


-k <int>
report up to <int> good alignments per read (default: 1)
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
hits guaranteed best stratum; ties broken by quality
hits in sub-optimal strata aren't reported (requires --best)


print wall-clock time taken by search phases
-B/--offbase <int> leftmost ref offset = <int> in bowtie output (default: 0)
print nothing but the alignments
write alignments to files, 1 map per reference
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
write entire ref name (default: only up to 1st space)


--snpphred <int>
Phred penalty for SNP when decoding colorspace (def: 30)
--snpfrac <dec>
approx. fraction of SNP bases (e.g. 0.001); sets --snpphred
print aligned colorspace seqs as colors, not decoded bases
print original colorspace quals, not decoded quals
keep nucleotides at extreme ends of decoded alignment


write hits in SAM format
--mapq <int>
default mapping quality (MAPQ) to print for SAM alignments
supppress header lines (starting with @) for SAM output
supppress @SQ header lines for SAM output
--sam-RG <text>
add <text> (usually "lab=value") to @RG line of SAM header


-o/--offrate <int> override offrate of index; must be >= index's offrate
-p/--threads <int> number of alignment threads to launch (default: 1)
use memory-mapped I/O for index; many 'bowtie's can share
use shared mem for index; many 'bowtie's can share


--seed <int>
seed for random number generator
verbose output (for debugging)
print version information and quit
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}