Bioinformatics Cover.

A graph-based approach to diploid genome assembly

By: Shilpa Garg, Mikko Rautiainen, Adam M Novak, Erik Garrison, Richard Durbin, Tobias Marschall

Abstract

Motivation

Constructing high-quality haplotype-resolved de novo assemblies of diploid genomes is important for revealing the full extent of structural variation and its role in health and disease. Current assembly approaches often collapse the two sequences into one haploid consensus sequence and, therefore, fail to capture the diploid nature of the organism under study. Thus, building an assembler capable of producing accurate and complete diploid assemblies, while being resource-efficient with respect to sequencing costs, is a key challenge to be addressed by the bioinformatics community.

Results

We present a novel graph-based approach to diploid assembly, which combines accurate Illumina data and long-read Pacific Biosciences (PacBio) data. We demonstrate the effectiveness of our method on a pseudo-diploid yeast genome and show that we require as little as 50× coverage Illumina data and 10× PacBio data to generate accurate and complete assemblies. Additionally, we show that our approach has the ability to detect and phase structural variants.

Availability and implementation

https://github.com/whatshap/whatshap

Supplementary information

Supplementary data are available at Bioinformatics online.

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Citation: Garg S, Rautiainen M, Novak AM, Garrison E, Durbin R, Marschall T. A graph-based approach to diploid genome assembly. Bioinformatics. 2018 Jun 27;34(13):i105-14.