NAME¶

sawriter - generate suffix arrays for nucleotide sequences

SYNOPSIS¶

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

sawriter fastaIn (writes to fastIn.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.

-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 more slow 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.

AUTHOR¶

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.