MsPAC: a tool for haplotype-phased structural variant detection

Bioinformatics. 2020 Feb 1;36(3):922-924. doi: 10.1093/bioinformatics/btz618.


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:

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Genome
  • Genomics*
  • Haplotypes
  • High-Throughput Nucleotide Sequencing*
  • Sequence Analysis, DNA
  • Software