Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Third-generation long-read sequencing and diploid assemblers yield high-quality genome assemblies.
• Highly heterozygous genomes pose challenges, leading to regional duplication instead of allelic variant consolidation.
• This duplication complicates downstream analyses like variant discovery and haplotype reconstruction.

Purpose of the Study:

• To develop an automated pipeline, Purge Haplotigs, for improving genome assemblies from third-generation sequencing data.
• To address the issue of mis-assigned allelic contigs in diploid genome assemblies.
• To facilitate manual curation of genome assemblies.

Main Methods:

• Developed Purge Haplotigs pipeline for third-generation sequencing assemblies.
• Utilized draft haplotype-fused or diploid assemblies, read alignments, and repeat annotations.
• Tested on simulated data and four diploid de novo assemblies, comparing with a similar tool.

Main Results:

• Purge Haplotigs successfully automated reassignment of allelic contigs.
• Processed haploid assemblies showed reduced duplication with maintained genome completeness.
• Processed diploid assemblies exhibited improved pairing of allelic contigs.

Conclusions:

• Purge Haplotigs enhances haploid and diploid representations in third-generation sequencing genome assemblies.
• The pipeline is fast, scalable for large genomes, and less prone to over-purging than alignment-only methods.
• The software is publicly available for use.