PT  - JOURNAL ARTICLE
AU  - Roland Faure
AU  - Nadège Guiglielmoni
AU  - Jean-François Flot
TI  - GraphUnzip: unzipping assembly graphs with long reads and Hi-C
AID  - 10.1101/2021.01.29.428779
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.01.29.428779
4099  - http://biorxiv.org/content/early/2021/02/01/2021.01.29.428779.short
4100  - http://biorxiv.org/content/early/2021/02/01/2021.01.29.428779.full
AB  - 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.Competing Interest StatementThe authors have declared no competing interest.