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

ABSTRACT:

Background

Recent developments in third-gen long read sequencing and diploid-aware assemblers have resulted in the rapid release of numerous reference-quality assemblies for diploid genomes. However, assembly of highly heterozygous genomes is still problematic when regional heterogeneity is so high that haplotype homology is not recognised during assembly. This results in regional duplication rather than consolidation into allelic variants and can cause issues with downstream analysis, for example variant discovery, or haplotype reconstruction using the diploid assembly with unpaired allelic contigs.

Results

A new pipeline-Purge Haplotigs-was developed specifically for third-gen sequencing-based assemblies to automate the reassignment of allelic contigs, and to assist in the

SUBMITTER: Roach MJ 

PROVIDER: S-EPMC6267036 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature