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)