sga-astat1

Compute myers' a-statistic for a set of contigs using the read alignments in in.bam

Usage

sga-astat [options] <in.bam>

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

Releases

Unchanged in 5 releases since Debian 9 (Stretch).

9–13