Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ
Year: 2020
Type: article
Abstract: Multiple whole-genome alignment is a challenging problem in bioinformatics. Despite many successes, current methods are not able to keep up with the growing number, length, and complexity of assembled genomes, especially when computational resources are limited. Approaches based on compacted de Bruijn graphs to identify and extend anchors into locally collinear blocks have potential for scalability, but current methods do not scale to mammalian genomes. We present an algorithm, SibeliaZ-LCB, for identifying collinear blocks in closely related genomes based on analysis of the de Bruijn graph. We further incorporate this into a multiple whole-genome alignment pipeline called SibeliaZ. SibeliaZ shows run-time improvements over other methods while maintaining accuracy. On sixteen recently-assembled strains of mice, SibeliaZ runs in under 16 hours on a single machine, while other tools did not run to completion for eight mice within a week. SibeliaZ makes a significant step towards improving scalability of multiple whole-genome alignment and collinear block reconstruction algorithms on a single machine.
Source: Nature Communications
Authors: Ilia Minkin, Paul Medvedev
Institution: Pennsylvania State University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $5,380
Awards: Y Chromosome Evolution, ABI Innovation: A Novel Framework for Detecting Genomic Structural Variation, G2353271501, III: Small: Reconstructing viral population without using a reference genome, XPS: FULL: DSD: End-to-end Acceleration of Genomic Workflows on Emerging Heterogeneous Supercomputers, CAREER: De Novo Assembly of Large Genomic Data
OpenAlex ID: W3111607156