ssw-align(1)

NAME

   ssw-align - fast Smith-Waterman aligner

SYNOPSIS

   ssw-align [options] ... <target.fasta> <query.fasta>(or <query.fastq>)

DESCRIPTION

   This  command  line  tool  uses  SSW,  a  fast SIMD optimized alignment
   library, to perform alignments on input files.

   The input files can be in FASTA or FASTQ format. Both target and  query
   files  can  contain multiple sequences. Each sequence in the query file
   will be aligned with all sequences in the target file.  If  the  target
   file  has  N  sequences and the query file has M sequences, the results
   will have M*N alignments.

OPTIONS

   -m N   N is a positive integer for  weight  match  in  genome  sequence
          alignment. [default: 2]

   -x N   N  is  a positive integer. -N will be used as weight mismatch in
          genome sequence alignment. [default: 2]

   -o N   N is a positive integer. -N will be used as the weight  for  the
          gap opening. [default: 3]

   -e N   N  is  a positive integer. -N will be used as the weight for the
          gap extension. [default: 1]

   -p     Do protein sequence alignment. Without this option, the ssw_test
          will do genome sequence alignment.

   -a  FILE  FILE  is  either  the  Blosum or Pam weight matrix. [default:
          Blosum50]

   -c     Return the alignment path.

   -f N   N is a positive integer. Only output  the  alignments  with  the
          Smith-Waterman score >= N.

   -r     The  best  alignment  will  be  picked between the original read
          alignment and the reverse complement read alignment.

   -s     Output in SAM format. [default: no header]

   -h     If -s is used, include header in SAM output.

OUTPUT FORMATS

   The software can output SAM format or BLAST like format results.  For a
   specification      of      the      SAM      format,     please     see
   http://samtools.sourceforge.net/SAM1.pdf. The additional optional field
   "ZS" indicates the suboptimal alignment score.

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