MsPAC: a tool for haplotype-phased structural variant detection

Abstract Summary While next-generation sequencing (NGS) has dramatically increased the availability of genomic data, phased genome assembly and structural variant (SV) analyses are limited by NGS read lengths. Long-read sequencing from Pacific Biosciences and NGS barcoding from 10x Genomics hold the...

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Bibliographic Details
Published inBioinformatics Vol. 36; no. 3; pp. 922 - 924
Main Authors Rodriguez, Oscar L, Ritz, Anna, Sharp, Andrew J, Bashir, Ali
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.02.2020
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Summary:Abstract Summary While next-generation sequencing (NGS) has dramatically increased the availability of genomic data, phased genome assembly and structural variant (SV) analyses are limited by NGS read lengths. Long-read sequencing from Pacific Biosciences and NGS barcoding from 10x Genomics hold the potential for far more comprehensive views of individual genomes. Here, we present MsPAC, a tool that combines both technologies to partition reads, assemble haplotypes (via existing software) and convert assemblies into high-quality, phased SV predictions. MsPAC represents a framework for haplotype-resolved SV calls that moves one step closer to fully resolved, diploid genomes. Availability and implementation https://github.com/oscarlr/MsPAC. Supplementary information Supplementary data are available at Bioinformatics online.
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ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btz618