Provided by: bowtie2_2.4.5-1_amd64 bug


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


       Bowtie 2 version 2.4.5 by Ben Langmead (,


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

              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.

       <i>    Files with interleaved paired-end FASTQ/FASTA reads

       <bam>  Files are unaligned BAM sorted by read name.

       <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)

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

       --tab5 query input files are TAB5 .tab5

       --tab6 query input files are TAB6 .tab6

       --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

       -F k:<int>,i:<int> query input files are continuous FASTA where reads
              are  substrings  (k-mers) extracted from a FASTA file <s> and aligned at offsets 1,
              1+i, 1+2i ... end of reference

       -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)

       --trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end
              If the read end is not specified then it defaults to 3 (0)

              qualities are Phred+33 (default)

              qualities are Phred+64

              qualities encoded as space-delimited integers

       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,1,1.15 (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

       -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,1,1.15)

       --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)

              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)

              do not allow 1 mismatch alignments before attempting to scan for the optimal seeded

              entire read must align; no clipping (on)


              local alignment; ends might be soft clipped (off)

       --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)

              look for multiple alignments, report best, with MAPQ


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


              report all alignments; very slow, MAPQ not meaningful

       -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)


       -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)

              suppress unpaired alignments for paired reads

              suppress discordant alignments for paired reads

              concordant when mates extend past each other

              not concordant when one mate alignment contains other

              not concordant when mates overlap at all


              Bowtie2  will, by default, attempt to align unpaired BAM reads.  Use this option to
              align paired-end reads instead.

              Preserve tags from the original BAM record by appending them  to  the  end  of  the
              corresponding SAM output.

              print wall-clock time taken by search phases

              print nothing to stderr except serious errors

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

              send metrics to stderr (off)

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

              suppress SAM records for unaligned reads

              suppress header lines, i.e. lines starting with @

              suppress @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.

              put '*' in SEQ and QUAL fields for secondary alignments.

              Suppress standard behavior of  truncating  readname  at  first  whitespace  at  the
              expense of generating non-standard SAM.

       --xeq  Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.

              Exclude soft-clipped bases when reporting TLEN

              Append FASTA/FASTQ comment to SAM record

       -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

              filter out reads that are bad according to QSEQ filter

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

              seed rand. gen. arbitrarily instead of using read attributes

              print version information and quit

              print this usage message