sawriter(1) generate suffix arrays for nucleotide sequences

SYNOPSIS

sawriter saOut  fastaIn [fastaIn2 fastaIn3 ...] [-blt p] [-4bit] [-larsson|-manmy|-kar|-mafe|-welter]

sawriter fastaIn (writes to fastaIn.sa)

OPTIONS

-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.