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.