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)