Wiki

Clone wiki

purge_haplotigs / Example images created by Purge Haplotigs

Example histograms:

PacBio subreads on a Diploid-phased assembly (Primary + Haplotigs)

Illumina PE reads on a Haploid assembly (Primary contigs)

Example dotplots:

A haplotig - Hopefully most of your reassigned haplotigs will look like this.

Contig is mostly haplotig - This example has part of the contig with a diploid level of coverage and part at haploid level with poor alignment to either reference (possibly hemizygous region).

Haplotig with many tandem repeats

Haplotig is palindrome

Contig circling through string graph 'knots' - while this may be a valid string graph path it will likely still confound short read mapping to the haploid assembly.

Updated