| SAWRITER(1) | User Commands | SAWRITER(1) |
NAME¶
sawriter - generate suffix arrays for nucleotide sequencesSYNOPSIS¶
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.
SEE ALSO¶
blasr(1) loadPulses(1) pls2fasta(1) samFilter(1) samtoh5(1) samtom4(1) sdpMatcher(1) toAfg(1)| July 2015 | sawriter 3ca7fe8 |