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.