SAWRITER(1) | User Commands | SAWRITER(1) |

# 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.

January 2019 | sawriter 5.3.2 |