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SDPMATCHER(1) User Commands SDPMATCHER(1)

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)

July 2015 sdpMatcher 3ca7fe8