RT Journal Article
SR Electronic
T1 GraphUnzip: unzipping assembly graphs with long reads and Hi-C
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.01.29.428779
DO 10.1101/2021.01.29.428779
A1 Roland Faure
A1 Nadège Guiglielmoni
A1 Jean-François Flot
YR 2021
UL http://biorxiv.org/content/early/2021/02/01/2021.01.29.428779.abstract
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.