NAME
sga-astat - Compute Myers' a-statistic for a set of contigs using the read alignments in in.bam
SYNOPSIS
sga-astat [options] <in.bam>
DESCRIPTION
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
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.