This is the command sawriter that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
sawriter - 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.
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