sawriter - generate suffix arrays for nucleotide sequences
sawriter saOut fastaIn [fastaIn2 fastaIn3 ...] [-blt p] [-larsson]
[-4bit] [-manmy] [-kar]
sawriter fastaIn (writes to fastIn.sa).
-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.
- Read in (one) fasta file as a compressed sequence file.
- (default) Uses the method of Larsson and Sadakane to build the array.
- Uses the method of MAnber and MYers to build the array (slower than
- and produces the same result. This is mainly for double checking the
correctness of larsson).
- 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)
- (disabled for now!) Use the lightweight construction algorithm from
Manzini and Ferragina
- 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
- Valid values are 7,32,64,111, and 2281.
This manpage was written by Andreas Tille for the Debian distribution and can be
used for any other usage of the program.