---
name: "sawriter"
section: "1"
platform: "linux"
package: "blasr"
version: "5.3.5+dfsg-7+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sawriter"
---

# sawriter(1)

generate suffix arrays for nucleotide sequences

## 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.