NAME

       sdpMatcher - nucleotide sequence matching using sparse dynamic programming

SYNOPSIS

       sdpMatcher  query  target k [-indelRate delta] [-showalign] [-printsw] [-noRefine] [-indel
       i] [-local] [-match m] [-sdpIndel i]

DESCRIPTION

       Performs sparse dynamic programming (SDP) between pairs of sequences as they are given  in
       two  FASTA files, called query and target for convenience. k is the size of the k-mer used
       for the SDP algorithm.

SEE ALSO

       blasr(1)  loadPulses(1)  pls2fasta(1)  samFilter(1)  samtoh5(1)   samtom4(1)   sawriter(1)
       toAfg(1)