Integrating Hi-C links with assembly graphs for chromosome-scale assembly.
Journal
PLoS computational biology
ISSN: 1553-7358
Titre abrégé: PLoS Comput Biol
Pays: United States
ID NLM: 101238922
Informations de publication
Date de publication:
08 2019
08 2019
Historique:
received:
11
01
2019
accepted:
18
07
2019
revised:
03
09
2019
pubmed:
23
8
2019
medline:
21
1
2020
entrez:
22
8
2019
Statut:
epublish
Résumé
Long-read sequencing and novel long-range assays have revolutionized de novo genome assembly by automating the reconstruction of reference-quality genomes. In particular, Hi-C sequencing is becoming an economical method for generating chromosome-scale scaffolds. Despite its increasing popularity, there are limited open-source tools available. Errors, particularly inversions and fusions across chromosomes, remain higher than alternate scaffolding technologies. We present a novel open-source Hi-C scaffolder that does not require an a priori estimate of chromosome number and minimizes errors by scaffolding with the assistance of an assembly graph. We demonstrate higher accuracy than the state-of-the-art methods across a variety of Hi-C library preparations and input assembly sizes. The Python and C++ code for our method is openly available at https://github.com/machinegun/SALSA.
Identifiants
pubmed: 31433799
doi: 10.1371/journal.pcbi.1007273
pii: PCOMPBIOL-D-19-00061
pmc: PMC6719893
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1007273Subventions
Organisme : NIAID NIH HHS
ID : R01 AI100947
Pays : United States
Organisme : NHGRI NIH HHS
ID : R44 HG009584
Pays : United States
Déclaration de conflit d'intérêts
Sergey Koren has received travel and accommodation expenses to speak at Oxford Nanopore Technologies conferences. Anthony Schmitt and Siddarth Selvaraj are employees of Arima Genomics, a company commercializing Hi-C DNA sequencing technologies.
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