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Clone wikipurge_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
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.
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