BOWTIE2-ALIGN(1)						   User Commands						  BOWTIE2-ALIGN(1)

NAME

       bowtie2-align - ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences

DESCRIPTION

       Bowtie 2 version 2.0.0-beta6 by Ben Langmead (blangmea@jhsph.edu) Usage:

	      bowtie2-align [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]

       <bt2-idx>
	      Index filename prefix (minus trailing .X.bt2).  NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.

       <m1>   Files with #1 mates, paired with files in <m2>.

       <m2>   Files with #2 mates, paired with files in <m1>.

       <r>    Files with unpaired reads.

       <sam>  File for SAM output (default: stdout)

	      <m1>,  <m2>,  <r>  can  be  comma-separated  lists  (no  whitespace) and can be specified many times.  E.g. '-U file1.fq,file2.fq -U
	      file3.fq'.

       Options (defaults in parentheses):

	      Input:

       -q     query input files are FASTQ .fq/.fastq (default)

       --qseq query input files are in Illumina's qseq format

       -f     query input files are (multi-)FASTA .fa/.mfa

       -r     query input files are raw one-sequence-per-line

       -c     <m1>, <m2>, <r> are sequences themselves, not files

       -s/--skip <int>
	      skip the first <int> reads/pairs in the input (none)

       -u/--upto <int>
	      stop after first <int> reads/pairs (no limit)

       -5/--trim5 <int>
	      trim <int> bases from 5'/left end of reads (0)

       -3/--trim3 <int>
	      trim <int> bases from 3'/right end of reads (0)

       --phred33
	      qualities are Phred+33 (default)

       --phred64
	      qualities are Phred+64

       --int-quals
	      qualities encoded as space-delimited integers

       Presets:
	      Same as:

	      For --end-to-end:

       --very-fast	      -D 5 -R 1 -N 0 -L 22 -i S,0,2.50

       --fast		      -D 10 -R 2 -N 0 -L 22 -i S,0,2.50

       --sensitive	      -D 15 -R 2 -N 0 -L 22 -i S,1,1.25 (default)

       --very-sensitive       -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

	      For --local:

       --very-fast-local      -D 5 -R 1 -N 0 -L 25 -i S,1,2.00

       --fast-local	      -D 10 -R 2 -N 0 -L 22 -i S,1,1.75

       --sensitive-local      -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)

       --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

	      Alignment:

       -N <int>
	      max # mismatches in seed alignment; can be 0 or 1 (0)

       -L <int>
	      length of seed substrings; must be >3, <32 (22)

       -i <func>
	      interval between seed substrings w/r/t read len (S,1,1.25)

       --n-ceil <func>
	      func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)

       --dpad <int>
	      include <int> extra ref chars on sides of DP table (15)

       --gbar <int>
	      disallow gaps within <int> nucs of read extremes (4)

       --ignore-quals
	      treat all quality values as 30 on Phred scale (off)

       --nofw do not align forward (original) version of read (off)

       --norc do not align reverse-complement version of read (off)

       --end-to-end
	      entire read must align; no clipping (on)

	      OR

       --local
	      local alignment; ends might be soft clipped (off)

	      Scoring:

       --ma <int>
	      match bonus (0 for --end-to-end, 2 for --local)

       --mp <int>
	      max penalty for mismatch; lower qual = lower penalty (6)

       --np <int>
	      penalty for non-A/C/G/Ts in read/ref (1)

       --rdg <int>,<int>
	      read gap open, extend penalties (5,3)

       --rfg <int>,<int>
	      reference gap open, extend penalties (5,3)

       --score-min <func> min acceptable alignment score w/r/t read length
	      (G,20,8 for local, L,-0.6,-0.6 for end-to-end)

	      Reporting:

       -M <int>
	      look for up to <int>+1 alns; report best, with MAPQ (5 for --end-to-end, 2 for --local)

	      OR

       -k <int>
	      report up to <int> alns per read; MAPQ not meaningful (off)

	      OR

       -a/--all
	      report all alignments; very slow (off)

	      Effort:

       -D <int>
	      give up extending after <int> failed extends in a row (15)

       -R <int>
	      for reads w/ repetitive seeds, try <int> sets of seeds (2)

	      Paired-end:

       -I/--minins <int>
	      minimum fragment length (0)

       -X/--maxins <int>
	      maximum fragment length (500)

       --fr/--rf/--ff	  -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)

       --no-mixed
	      suppress unpaired alignments for paired reads

       --no-discordant
	      suppress discordant alignments for paired reads

       --no-dovetail
	      not concordant when mates extend past each other

       --no-contain
	      not concordant when one mate alignment contains other

       --no-overlap
	      not concordant when mates overlap at all

	      Output:

       -t/--time
	      print wall-clock time taken by search phases

       --quiet
	      print nothing to stderr except serious errors

       --met-file <path>
	      send metrics to file at <path> (off)

       --met-stderr
	      send metrics to stderr (off)

       --met <int>
	      report internal counters & metrics every <int> secs (1)

       --no-unal
	      supppress SAM records for unaligned reads

       --no-head
	      supppress header lines, i.e. lines starting with @

       --no-sq
	      supppress @SQ header lines

       --rg-id <text>
	      set read group id, reflected in @RG line and RG:Z: opt field

       --rg <text>
	      add <text> ("lab:value") to @RG line of SAM header.  Note: @RG line only printed when --rg-id is set.

	      Performance:

       -o/--offrate <int> override offrate of index; must be >= index's offrate

       -p/--threads <int> number of alignment threads to launch (1)

       --reorder
	      force SAM output order to match order of input reads

       --mm   use memory-mapped I/O for index; many 'bowtie's can share

	      Other:

       --qc-filter
	      filter out reads that are bad according to QSEQ filter

       --seed <int>
	      seed for random number generator (0)

       --version
	      print version information and quit

       -h/--help
	      print this usage message

       64-bit Built on lxcsid Fri Jun  1 20:11:44 UTC 2012 Compiler: gcc version 4.7.0 (Debian 4.7.0-8) Options: -O3  -m64  -msse2  -funroll-loops
       -g3 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

bowtie2-align version 2.0.0-beta6				     June 2012							  BOWTIE2-ALIGN(1)