Provided by: blasr_5.3+0-2_amd64

**NAME**

sawriter - generate suffix arrays for nucleotide sequences

**SYNOPSIS**

sawritersaOutfastaIn[fastaIn2fastaIn3...] [-bltp] [-4bit] [-larsson|-manmy|-kar|-mafe|-welter]sawriterfastaIn(writes to fastaIn.sa)

**OPTIONS**

-bltpBuild a lookup table on prefixes of lengthp. This speeds up lookups considerably (more than the LCP table), but misses matches less thanpwhen searching.-4bitRead in (one) fasta file as a compressed sequence file.Methods-larsson(default) Uses the method of Larsson and Sadakane to build the array.-mamyUses 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).-karkUse 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-welterUse lightweight (sort of light) suffix array construction. This is a bit more slow than normal larsson.-welterweightNuse a difference cover of sizeNfor building the suffix array. Valid values are 7,32,64,111, and 2281.

**SEE** **ALSO**

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