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

By Jay Ghurye, Arang Rhie, Brian Walenz, Anthony D. Schmitt, Siddarth Selvaraj, Mihai Pop, Adam M. Phillippy, Sergey Koren. bioRxiv, 2018

637 citations recorded by the source corpus.

Motivation 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. Results 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. Availability and Implementation The Python and C++ code for our method is openly available at https://github.com/machinegun/SALSA Contact sergey.koren@nih.gov, adam.phillippy@nih.gov Supplementary information Not available online.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/55228e700ae3a1fefffcb7f7ae5d2bf51fdd4ec7

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Citations in the corpus

Long-read human genome sequencing and its applications (2020, neutral): “…deoxynucleoside triphosphate that is imaged to identify the base and then cleaved before the process is repeated to determine the order and identity of each base in the DNa strand. contigs in broken genome assemblies 21 , phase haplotypes 22 , and lead to the discovery of structural variation 23 .”
YaHS: yet another Hi-C scaffolding tool (2022, neutral): “…tools have been developed for the construction of chromosome-scale assembly with Hi-C data including LACHESIS (Burton et al. , 2013), HiRise (Putnam et al. , 2016), 3D-DNA (Dudchenko et al. , 2017), ALLHiC (Zhang et al. , 2019), SALSA2 (Ghurye et al. , 2019) and pin_hic (Guan et al. , 2021).”
Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing (2021, positive): “RagTag analyzes this graph to resolve ambiguous paths, optionally using Hi-C data to re-weight the edges [17].”
Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs (2022, methodology): “Importantly, gfastats can convert AGP to GFA paths, allowing the output of any automated scaffolding tool such as Bionano Solve (https://bionanogenomics.com/downloads/bionano-solve/) SALSA2 [10] to be integrated in the graph.”