GraphUnzip: unzipping assembly graphs with long reads and Hi-C

Abstract

Long reads and Hi-C have revolutionized the field of genome assembly as they have made highly continuous assemblies accessible for challenging genomes. As haploid chromosome-level assemblies are now commonly achieved for all types of organisms, phasing assemblies has become the new frontier for genome reconstruction. Several tools have already been released using long reads and/or Hi-C to phase assemblies, but they all start from a linear sequence, and are ill-suited for non-model organisms with high levels of heterozygosity. We present GraphUnzip, a fast, memory-efficient and accurate tool to unzip assembly graphs into their constituent haplotypes using long reads and/or Hi-C data. As GraphUnzip only connects sequences in the assembly graph that already had a potential link based on overlaps, it yields high-quality gap-less supercontigs. To demonstrate the efficiency of GraphUnzip, we tested it on a simulated diploid Escherichia coli genome, and on two real datasets for the genomes of the rotifer Adineta vaga and the potato Solanum tuberosum. In all cases, GraphUnzip yielded highly continuous phased assemblies.

Portable nanopore-sequencing technology: Trends in development and applications

“…In contrast to previous work, in Faure et al (2021) , the authors present GraphUnzip, a fast, memory-efficient, and accurate tool that generates high-quality gap-less supercontigs by connecting only sequences that overlap potential links. In Murigneux et al (2021) , the authors present an easy-access, integrated solution for attaining high-quality bacterial genomes by combining ONT with Illumina sequencing to create MicroPIPE, an end-to-end process for assembling bacterial genomes.…”

A deep dive into genome assemblies of non-vertebrate animals

“…Hapo-G [162]). As Hi-C has demonstrated its efficiency to scaffold haploid assemblies, the principles were further exploited in ALLHiC [293], GraphUnzip [294] and FALCON-Phase [295] to phase assemblies while increasing their contiguity: as alleles from one haplotype belong to one chromosome, these alleles have higher Hi-C interaction frequencies together than with alleles from alternative haplotypes.…”

A Deep Dive into Genome Assemblies of Non-vertebrate Animals

“…Hapo-G [161]). As Hi-C has already demonstrated its efficiency to scaffold haploid assemblies, the principles were further exploited in ALLHiC [288], GraphUnzip [289] and FALCON-Phase [290] to phase assemblies while increasing their contiguity: as alleles from one haplotype belong to one chromosome, these alleles have higher Hi-C interaction frequencies together than with alleles from alternative haplotypes.…”