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

Abstract

BackgroundRecent 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.ResultsA 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 manual curation of genome assemblies. The pipeline uses a draft haplotype-fused assembly or a diploid assembly, read alignments, and repeat annotations to identify allelic variants in the primary assembly. The pipeline was tested on a simulated dataset and on four recent diploid (phased) de novo assemblies from third-generation long-read sequencing, and compared with a similar tool. After processing with Purge Haplotigs, haploid assemblies were less duplicated with minimal impact on genome completeness, and diploid assemblies had more pairings of allelic contigs.ConclusionsPurge Haplotigs improves the haploid and diploid representations of third-gen sequencing based genome assemblies by identifying and reassigning allelic contigs. The implementation is fast and scales well with large genomes, and it is less likely to over-purge repetitive or paralogous elements compared to alignment-only based methods. The software is available at https://bitbucket.org/mroachawri/purge_haplotigs under a permissive MIT licence.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2485-7) contains supplementary material, which is available to authorized users.

A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System

“…Data were assembled with FALCON-Unzip [21] using pb-falcon version 0. https://github.com/PacificBiosciences/pbbioconda. We screened the primary assembly for duplicate haplotypes using Purge Haplotigs (bioconda v1.0.4) [48]. Purge Haplotigs identifies candidate haplotigs in the primary contigs using PacBio read coverage depth and contig alignments.…”

New genome assemblies reveal patterns of domestication and adaptation acrossBrettanomyces(Dekkera) species

“…Predicted genome completeness was high for the haploid assemblies, with between 3.8 % (B. naardenensis) and 7.2 % (B. anomalus) missing BUSCOs. The assemblies were processed with Purge Haplotigs (Roach et al, 2018) to remove duplicated and artifactual contigs. Duplication was low for not only the homozygous strains but also for the heterozygous B. anomalus assembly with between 0.5 % (B. nanus) and 1.2 % (B. anomalus) duplicate BUSCOs.…”

“…Paired-end and mate-pair reads were mapped with BWA-MEM v0.7.12-r1039 (Li, 2013) and Bowtie2 v2.2.9 (Langmead and Salzberg, 2012) respectively; base-call polishing was then performed with Pilon v1.22 (Walker et al, 2014). Finally, raw Nanopore reads were mapped to the base-call-polished assemblies and Purge Haplotigs v1.0.1 (Roach et al, 2018) was used to remove any duplicate or artefactual contigs.…”

“…Pairwise synteny blocks were generated between the reference B. bruxellensis assembly and the other haploid assemblies, as well as between the B. naardenensis and B. nanus assemblies. Contigs were placed in chromosome order using Purge Haplotigs (Roach et al, 2018) to generate placement files that were then used to rearrange contigs. Alignments between the assemblies were calculated using NUCmer with sensitive parameters (-b 500 -c 40 -d 0.5 -g 200 -l 12).…”

“…Predicted genome completeness was high for the haploid assemblies, with between 3.8 % (B. naardenensis) and 7.2 % (B. anomalus) missing BUSCOs. The assemblies were processed with Purge Haplotigs [25] to remove duplicated and artifactual contigs.…”