Integrating Hi-C links with assembly graphs for chromosome-scale assembly

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, th...

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Bibliographic Details
Published in:PLoS computational biology Vol. 15; no. 8; p. e1007273
Main Authors: Ghurye, Jay, Rhie, Arang, Walenz, Brian P., Schmitt, Anthony, Selvaraj, Siddarth, Pop, Mihai, Phillippy, Adam M., Koren, Sergey
Format: Journal Article
Language:English
Published: United States Public Library of Science 01.08.2019
Public Library of Science (PLoS)
Subjects:
Algorithms
Animals
Assembly
Bioinformatics
Biology and Life Sciences
Biosynthesis
Chromosome number
Chromosome replication
Chromosomes
Chromosomes, Human - genetics
Computational Biology
Computer and Information Sciences
Computer science
Computer Simulation
Databases, Nucleic Acid - statistics & numerical data
DNA sequencing
Gene sequencing
Genome, Human
Genomes
Genomic Library
Genomics
Genomics - methods
Genomics - statistics & numerical data
High-Throughput Nucleotide Sequencing - methods
High-Throughput Nucleotide Sequencing - statistics & numerical data
Humans
Informatics
Inversions
Methods
Open source software
Research and Analysis Methods
Scaffolding
Sequence Analysis, DNA - methods
Sequence Analysis, DNA - statistics & numerical data
Software
Source code
Technology application
Whole genome sequencing
United States
United States > US
Maryland
California
ISSN:1553-7358, 1553-734X, 1553-7358
Online Access:Get full text
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Description
Summary: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.
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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.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1007273