DESCRIPTION
Bowtie 2 version 2.0.0-beta6 by Ben Langmead ([email protected]) 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
- --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
-
- 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
- --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
-
- 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
- -p/--threads <int> number of alignment threads to launch (1)
-
- 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}