Provided by: blasr_5.3+0-2_amd64
sawriter - generate suffix arrays for nucleotide sequences
sawriter saOut fastaIn [fastaIn2 fastaIn3 ...] [-blt p] [-4bit] [-larsson|-manmy|-kar|-mafe|-welter] sawriter fastaIn (writes to fastaIn.sa)
-blt p Build a lookup table on prefixes of length p. This speeds up lookups considerably (more than the LCP table), but misses matches less than p when searching. -4bit Read in (one) fasta file as a compressed sequence file. Methods -larsson (default) Uses the method of Larsson and Sadakane to build the array. -mamy Uses the method of MAnber and MYers to build the array (slower than larsson, and produces the same result. This is mainly for double checking the correctness of larsson). -kark Use Karkkainen DS3 method for building the suffix array. This will probably be slower than larsson, but takes only an extra N/(sqrt 3) extra space. -mafe (disabled for now!) Use the lightweight construction algorithm from Manzini and Ferragina -welter Use lightweight (sort of light) suffix array construction. This is a bit more slow than normal larsson. -welterweight N use a difference cover of size N for building the suffix array. Valid values are 7,32,64,111, and 2281.
blasr(1) loadPulses(1) pls2fasta(1) samFilter(1) samtoh5(1) samtom4(1) sdpMatcher(1) toAfg(1)