sawriter1
Generate suffix arrays for nucleotide sequences
Usage
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.
-welterweightN use a difference cover of size N for building the suffix array.-
Valid values are 7,32,64,111, and 2281.
Releases
5 releases since Debian 9 (Stretch); the text changed 1 time.
-larsson since Debian 10 (Buster).