Man page - sga-bam2de(1)

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Package: sga
apt-get install sga

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sga-bam2de - Make a distance estimate file from a bam file of reads aligned to contigs

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.