--- name: "bowtie2-align" section: "1" platform: "linux" package: "bowtie2" version: "2.0.0-beta6-3" release: "Debian 7 (Wheezy)" platforms: ["linux"] url: "https://new.carta.tech/bowtie2-align" --- # bowtie2-align(1) ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences ## 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** \ {-1 \ **-2** \ \| **-U** \} \[-S \\] - \ Index filename prefix (minus trailing .X.bt2). NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. - \ Files with #1 mates, paired with files in \. - \ Files with #2 mates, paired with files in \. - \ Files with unpaired reads. - \ File for SAM output (default: stdout) - \, \, \ 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** \, \, \ are sequences themselves, not files - **-s**/--skip \ skip the first \ reads/pairs in the input (none) - **-u**/--upto \ stop after first \ reads/pairs (no limit) - **-5**/--trim5 \ trim \ bases from 5'/left end of reads (0) - **-3**/--trim3 \ trim \ 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** \ max # mismatches in seed alignment; can be 0 or 1 (0) - **-L** \ length of seed substrings; must be \>3, \<32 (22) - **-i** \ interval between seed substrings w/r/t read len (S,1,1.25) - **--n-ceil** \ func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) - **--dpad** \ include \ extra ref chars on sides of DP table (15) - **--gbar** \ disallow gaps within \ 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** \ match bonus (0 for **--end-to-end**, 2 for **--local**) - **--mp** \ max penalty for mismatch; lower qual = lower penalty (6) - **--np** \ penalty for non-A/C/G/Ts in read/ref (1) - **--rdg** \,\ read gap open, extend penalties (5,3) - **--rfg** \,\ reference gap open, extend penalties (5,3) - **--score-min** \ 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** \ look for up to \+1 alns; report best, with MAPQ (5 for **--end-to-end**, 2 for **--local**) - OR - **-k** \ report up to \ alns per read; MAPQ not meaningful (off) - OR - **-a**/--all report all alignments; very slow (off) - Effort: - **-D** \ give up extending after \ failed extends in a row (15) - **-R** \ for reads w/ repetitive seeds, try \ sets of seeds (2) - Paired-end: - **-I**/--minins \ minimum fragment length (0) - **-X**/--maxins \ 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** \ send metrics to file at \ (off) - **--met-stderr** send metrics to stderr (off) - **--met** \ report internal counters & metrics every \ 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** \ set read group id, reflected in @RG line and RG:Z: opt field - **--rg** \ add \ ("lab:value") to @RG line of SAM header. Note: @RG line only printed when **--rg-id** is set. - Performance: **-o**/--offrate \ override offrate of index; must be \>= index's offrate **-p**/--threads \ 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** \ 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}