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
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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.