sga-astat1

Usage

Overview

The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.

SGA is a de novo assembler for DNA sequence reads. It is based on Gene Myers' string graph formulation of assembly and uses the FM-index/Burrows-Wheeler transform to efficiently find overlaps between sequence reads.

Options

-m=INT

only compute a-stat for contigs at least INT bases in length

-b=INT

use the longest INT contigs to perform the initial estimate of the arrival rate (default: 20)

-n=INT

perform INT bootstrap iterations of the estimate

-g=INT

use INT as the genome size instead of estimating it

--no-duplicates

do not use duplicate reads to calculate statistics