DESCRIPTION

sga-bam2de.pl - Make a distance estimate file from a bam file of reads aligned to contigs sga-bam2de.pl -n N --prefix lib300 lib300.bam Options:

-n N

Minimum number of pairs required to consider two contigs linked

-m LEN

Only find links between contigs with length at least LEN bp (default: 200)

-t NUM

Use NUM threads for computing the distance estimates

--prefix NAME

Use NAME as the prefix for the outfiles

--mind D

Set the minimum distance estimate to test to be D. This should be a negative number if contigs are expected to overlap. Defaults to -99bp.

--mina N

Set the minimum alignment length to be N.

--help

This help output.