Provided by: bowtie2_2.1.0-2_amd64 bug


       bowtie2 - wrapper for bowtie2-align


       No  index,  query,  or  output  file  specified!   Bowtie  2 version 2.1.0 by Ben Langmead
       (, Usage:

              bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-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>.  Could be gzip'ed (extension: .gz)
              or bzip2'ed (extension: .bz2).

       <m2>   Files with #2 mates, paired with files in <m1>.  Could be gzip'ed (extension:  .gz)
              or bzip2'ed (extension: .bz2).

       <r>    Files  with  unpaired  reads.   Could  be  gzip'ed  (extension:  .gz)  or  bzip2'ed
              (extension: .bz2).

       <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)

       --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)

              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)

              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

              not concordant when mates extend past each other

              not concordant when one mate alignment contains other

              not concordant when mates overlap at all


              print wall-clock time taken by search phases

       --un <path>
              write unpaired reads that didn't align to <path>

       --al <path>
              write unpaired reads that aligned at least once to <path>

       --un-conc <path>
              write pairs that didn't align concordantly to <path>

       --al-conc <path>
              write pairs that aligned concordantly at least once to <path>

              (Note:  for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
              --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2  compress  output.)
              --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-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.

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


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

       -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)

       --non-deterministic seed rand. gen. arbitrarily instead of using read attributes

              print version information and quit

              print this usage message

       bowtie2-align exited with value 1