.TH SGA-ASTAT "1" "September 2016" "sga-astat 0.10.15" "User Commands"
.SH NAME
sga-astat \- Compute Myers' a-statistic for a set of contigs using the read alignments in in.bam
.SH SYNOPSIS
.B sga-astat
\fI[options]\fR \fI<in.bam>\fR
.SH DESCRIPTION
The major goal of SGA is to be very memory efficient, which is achieved by
using a compressed representation of DNA sequence reads.
.P
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.
.SH OPTIONS
.TP
-m=INT
only compute a-stat for contigs at least INT bases in length
.TP
-b=INT
use the longest INT contigs to perform the initial estimate
of the arrival rate (default: 20)
.TP
-n=INT
perform INT bootstrap iterations of the estimate
.TP
-g=INT
use INT as the genome size instead of estimating it
.TP
--no-duplicates
do not use duplicate reads to calculate statistics
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.