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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 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.

SUBMITTER: Rodriguez OL

PROVIDER: S-EPMC7523683 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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MsPAC: a tool for haplotype-phased structural variant detection.

Rodriguez Oscar L OL Ritz Anna A Sharp Andrew J AJ Bashir Ali A

Bioinformatics (Oxford, England) 20200201 3

<h4>Summary</h4>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 con ...[more]

PMID: 31397844

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