Provided by: bowtie2_2.3.4.2-1_amd64 bug

NAME

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

DESCRIPTION

       Bowtie 2 version 2.3.4.2 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> | --interleaved  <i>}  [-S
       <sam>]

       <bt2-idx>
              Index  filename  prefix  (minus  trailing  .X.bt2l).   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 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)

       --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)

       --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)

       --no-1mm-upfront
              do not allow 1 mismatch alignments before attempting to scan for the optimal seeded
              alignments

       --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

       --dovetail
              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
              suppress SAM records for unaligned reads

       --no-head
              suppress header lines, i.e. lines starting with @

       --no-sq
              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.

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

       --sam-no-qname-trunc 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.

       --soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN

   Performance:
       -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