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Integrating Hi-C links with assembly graphs for chromosome-scale assembly
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Integrating Hi-C links with assembly graphs for chromosome-scale assembly
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Journal Article
Integrating Hi-C links with assembly graphs for chromosome-scale assembly
2019
Overview
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.
Publisher
Public Library of Science,Public Library of Science (PLoS)
Subject
/ Animals
/ Assembly
/ Chromosomes, Human - genetics
/ Computer and Information Sciences
/ Databases, Nucleic Acid - statistics & numerical data
/ Genomes
/ Genomics
/ Genomics - statistics & numerical data
/ High-Throughput Nucleotide Sequencing - methods
/ High-Throughput Nucleotide Sequencing - statistics & numerical data
/ Humans
/ Methods
/ Research and Analysis Methods
/ Sequence Analysis, DNA - methods
/ Sequence Analysis, DNA - statistics & numerical data
/ Software
