.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH BOWTIE "1" "October 2016" "bowtie version 1.1.2" "User Commands"
.SH NAME
bowtie \- ultrafast memory-efficient short read aligner
.SH DESCRIPTION
Usage:
bowtie [options]* <ebwt> {\-1 <m1> \fB\-2\fR <m2> | \fB\-\-12\fR <r> | <s>} [<hit>]
.TP
<m1>
Comma\-separated list of files containing upstream mates (or the
sequences themselves, if \fB\-c\fR is set) paired with mates in <m2>
.TP
<m2>
Comma\-separated list of files containing downstream mates (or the
sequences themselves if \fB\-c\fR is set) paired with mates in <m1>
.TP
<r>
Comma\-separated list of files containing Crossbow\-style reads.  Can be
a mixture of paired and unpaired.  Specify "\-" for stdin.
.TP
<s>
Comma\-separated list of files containing unpaired reads, or the
sequences themselves, if \fB\-c\fR is set.  Specify "\-" for stdin.
.TP
<hit>
File to write hits to (default: stdout)
.SS "Input:"
.TP
\fB\-q\fR
query input files are FASTQ .fq/.fastq (default)
.TP
\fB\-f\fR
query input files are (multi\-)FASTA .fa/.mfa
.TP
\fB\-r\fR
query input files are raw one\-sequence\-per\-line
.TP
\fB\-c\fR
query sequences given on cmd line (as <mates>, <singles>)
.TP
\fB\-C\fR
reads and index are in colorspace
.TP
\fB\-Q\fR/\-\-quals <file>
QV file(s) corresponding to CSFASTA inputs; use with \fB\-f\fR \fB\-C\fR
.TP
\fB\-\-Q1\fR/\-\-Q2 <file>
same as \fB\-Q\fR, but for mate files 1 and 2 respectively
.TP
\fB\-s\fR/\-\-skip <int>
skip the first <int> reads/pairs in the input
.TP
\fB\-u\fR/\-\-qupto <int>
stop after first <int> reads/pairs (excl. skipped reads)
.TP
\fB\-5\fR/\-\-trim5 <int>
trim <int> bases from 5' (left) end of reads
.TP
\fB\-3\fR/\-\-trim3 <int>
trim <int> bases from 3' (right) end of reads
.TP
\fB\-\-phred33\-quals\fR
input quals are Phred+33 (default)
.TP
\fB\-\-phred64\-quals\fR
input quals are Phred+64 (same as \fB\-\-solexa1\fR.3\-quals)
.TP
\fB\-\-solexa\-quals\fR
input quals are from GA Pipeline ver. < 1.3
.TP
\fB\-\-solexa1\fR.3\-quals
input quals are from GA Pipeline ver. >= 1.3
.TP
\fB\-\-integer\-quals\fR
qualities are given as space\-separated integers (not ASCII)
.TP
\fB\-\-large\-index\fR
force usage of a 'large' index, even if a small one is present
.SS "Alignment:"
.TP
\fB\-v\fR <int>
report end\-to\-end hits w/ <=v mismatches; ignore qualities
.IP
or
.HP
\fB\-n\fR/\-\-seedmms <int> max mismatches in seed (can be 0\-3, default: \fB\-n\fR 2)
.TP
\fB\-e\fR/\-\-maqerr <int>
max sum of mismatch quals across alignment for \fB\-n\fR (def: 70)
.HP
\fB\-l\fR/\-\-seedlen <int> seed length for \fB\-n\fR (default: 28)
.TP
\fB\-\-nomaqround\fR
disable Maq\-like quality rounding for \fB\-n\fR (nearest 10 <= 30)
.TP
\fB\-I\fR/\-\-minins <int>
minimum insert size for paired\-end alignment (default: 0)
.TP
\fB\-X\fR/\-\-maxins <int>
maximum insert size for paired\-end alignment (default: 250)
.HP
\fB\-\-fr\fR/\-\-rf/\-\-ff     \fB\-1\fR, \fB\-2\fR mates align fw/rev, rev/fw, fw/fw (default: \fB\-\-fr\fR)
.TP
\fB\-\-nofw\fR/\-\-norc
do not align to forward/reverse\-complement reference strand
.TP
\fB\-\-maxbts\fR <int>
max # backtracks for \fB\-n\fR 2/3 (default: 125, 800 for \fB\-\-best\fR)
.TP
\fB\-\-pairtries\fR <int>
max # attempts to find mate for anchor hit (default: 100)
.TP
\fB\-y\fR/\-\-tryhard
try hard to find valid alignments, at the expense of speed
.TP
\fB\-\-chunkmbs\fR <int>
max megabytes of RAM for best\-first search frames (def: 64)
.SS "Reporting:"
.TP
\fB\-k\fR <int>
report up to <int> good alignments per read (default: 1)
.TP
\fB\-a\fR/\-\-all
report all alignments per read (much slower than low \fB\-k\fR)
.TP
\fB\-m\fR <int>
suppress all alignments if > <int> exist (def: no limit)
.TP
\fB\-M\fR <int>
like \fB\-m\fR, but reports 1 random hit (MAPQ=0); requires \fB\-\-best\fR
.TP
\fB\-\-best\fR
hits guaranteed best stratum; ties broken by quality
.TP
\fB\-\-strata\fR
hits in sub\-optimal strata aren't reported (requires \fB\-\-best\fR)
.SS "Output:"
.TP
\fB\-t\fR/\-\-time
print wall\-clock time taken by search phases
.HP
\fB\-B\fR/\-\-offbase <int> leftmost ref offset = <int> in bowtie output (default: 0)
.TP
\fB\-\-quiet\fR
print nothing but the alignments
.TP
\fB\-\-refout\fR
write alignments to files refXXXXX.map, 1 map per reference
.TP
\fB\-\-refidx\fR
refer to ref. seqs by 0\-based index rather than name
.TP
\fB\-\-al\fR <fname>
write aligned reads/pairs to file(s) <fname>
.TP
\fB\-\-un\fR <fname>
write unaligned reads/pairs to file(s) <fname>
.TP
\fB\-\-max\fR <fname>
write reads/pairs over \fB\-m\fR limit to file(s) <fname>
.TP
\fB\-\-suppress\fR <cols>
suppresses given columns (comma\-delim'ed) in default output
.TP
\fB\-\-fullref\fR
write entire ref name (default: only up to 1st space)
.SS "Colorspace:"
.TP
\fB\-\-snpphred\fR <int>
Phred penalty for SNP when decoding colorspace (def: 30)
.IP
or
.TP
\fB\-\-snpfrac\fR <dec>
approx. fraction of SNP bases (e.g. 0.001); sets \fB\-\-snpphred\fR
.TP
\fB\-\-col\-cseq\fR
print aligned colorspace seqs as colors, not decoded bases
.TP
\fB\-\-col\-cqual\fR
print original colorspace quals, not decoded quals
.TP
\fB\-\-col\-keepends\fR
keep nucleotides at extreme ends of decoded alignment
.SS "SAM:"
.TP
\fB\-S\fR/\-\-sam
write hits in SAM format
.TP
\fB\-\-mapq\fR <int>
default mapping quality (MAPQ) to print for SAM alignments
.TP
\fB\-\-sam\-nohead\fR
supppress header lines (starting with @) for SAM output
.TP
\fB\-\-sam\-nosq\fR
supppress @SQ header lines for SAM output
.TP
\fB\-\-sam\-RG\fR <text>
add <text> (usually "lab=value") to @RG line of SAM header
.SS "Performance:"
.HP
\fB\-o\fR/\-\-offrate <int> override offrate of index; must be >= index's offrate
.HP
\fB\-p\fR/\-\-threads <int> number of alignment threads to launch (default: 1)
.TP
\fB\-\-mm\fR
use memory\-mapped I/O for index; many 'bowtie's can share
.TP
\fB\-\-shmem\fR
use shared mem for index; many 'bowtie's can share
.SS "Other:"
.TP
\fB\-\-seed\fR <int>
seed for random number generator
.TP
\fB\-\-verbose\fR
verbose output (for debugging)
.TP
\fB\-\-version\fR
print version information and quit
.TP
\fB\-h\fR/\-\-help
print this usage message
.PP
64\-bit
Built on Debian\-reproducible
Fri, 14 Oct 2016 20:53:17 +0200
Compiler: gcc version 6.2.0 20161010
Options: \fB\-O3\fR  \fB\-Wl\fR,\-\-hash\-style=both \fB\-Wdate\-time\fR \fB\-D_FORTIFY_SOURCE\fR=\fI\,2\/\fR \fB\-g\fR \fB\-O2\fR \fB\-fdebug\-prefix\-map=\fR.=. \fB\-fPIE\fR \fB\-fstack\-protector\-strong\fR \fB\-Wformat\fR \fB\-Werror\fR=\fI\,format\-security\/\fR  \fB\-g\fR \fB\-O2\fR \fB\-fdebug\-prefix\-map=\fR.=. \fB\-fPIE\fR \fB\-fstack\-protector\-strong\fR \fB\-Wformat\fR \fB\-Werror\fR=\fI\,format\-security\/\fR  \fB\-fPIE\fR \fB\-pie\fR \fB\-Wl\fR,\-z,relro \fB\-Wl\fR,\-z,now
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}