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diriano / ploidyNGS

Explore ploidy levels from NGS data alone
GNU General Public License v3.0
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Is it need a long time? #2

Closed tiramisutes closed 7 years ago

tiramisutes commented 7 years ago

My program was hanging out for a long time in the XXXsorted.bam.bai file, but no any error or increased of this XXXsorted.bam.bai file size.

diriano commented 7 years ago

Dear tiramisutes,

Thanks for the interest in our software.

The running time of ploidyNGS depends on both the size of your genome and the number of reads. If you have a large genome, I recommend the you run ploidyNGS on a single contigs/chromosome. If you have a very large coverage, subsampling will also help here, we have seen that 100x coverage is enough to get a good idea about ploidy levels.

Cheers, Diego

tiramisutes commented 7 years ago

Dear Thanks for the reply. Can I get my sorted bam file via alignment reads to contigs.fa or scaffolds.fa, which is the resulted of genomes assembly software, such as SOAPdenovo, and then input the ploidyNGS to get final results?

Best

diriano commented 7 years ago

Yes you can.