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Bioinformatics. 2019 Aug 9. pii: btz618. doi: 10.1093/bioinformatics/btz618. [Epub ahead of print]

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

Author information

1
Department of Genetics and Data Science, Icahn School of Medicine at Mount Sinai, New York, USA.
2
Biology Department, Reed College, Portland, USA.

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 (PacBio) and NGS barcoding from 10X Genomics (10X) 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:

https://github.com/oscarlr/MsPAC.

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