purge_haplotigs readhist: unable to distinguishing the two histogram peaks

[uceleste]

Hi All,

I'm running purge_haplotigs on my heterozygous diploid-phased assembly (primary + haplotigs) using pacbio reads:

$ minimap2 -ax map-pb p_h.fasta pacbio.fasta -t 30 | samtools sort -@ 30 -m 1G -o aligned.bam -T tmp.aln

$ purge_haplotigs readhist -b aligned.bam -g p_h.fasta -t 30

I obtained the coverage histogram but I am not able to properly distinguish the to peaks. Please find the attached histogram.

What could be the reason? Which low, mid and high cutoff values should I take?

Cheers

[mroach-awri]

You're half coverage peak is at 30, the second peak is at 60 (it just looks like a shoulder on the first peak). I'd also recommend using the latest version from https://bitbucket.org/mroachawri/purge_haplotigs/