NAME

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

DESCRIPTION

       No index, query, or output file  specified!   Bowtie  2  version  2.1.0  by  Ben  Langmead
       (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) 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,1,1.15 (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

              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,1,1.15)

       --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)

       --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:

       (default)
              look for multiple alignments, report best, with MAPQ

              OR

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

              OR

       -a/--all
              report all alignments; very slow, MAPQ not meaningful

              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-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.

       --omit-sec-seq
              put '*' in SEQ and QUAL fields for secondary alignments.

              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)

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

       --version
              print version information and quit

       -h/--help
              print this usage message

       *** Warning *** 'bowtie2-align' was run directly.  It is  recommended  that  you  run  the
       wrapper script 'bowtie2' instead.