MsPAC: a tool for haplotype-phased structural variant detection

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  • Oscar L Rodriguez
    Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA
  • Anna Ritz
    Biology Department, Reed College , Portland, OR 97202, USA
  • Andrew J Sharp
    Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA
  • Ali Bashir
    Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA
  • Janet Kelso
    editor

抄録

<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Summary</jats:title> <jats:p>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.</jats:p> </jats:sec> <jats:sec> <jats:title>Availability and implementation</jats:title> <jats:p>https://github.com/oscarlr/MsPAC.</jats:p> </jats:sec> <jats:sec> <jats:title>Supplementary information</jats:title> <jats:p>Supplementary data are available at Bioinformatics online.</jats:p> </jats:sec>

収録刊行物

  • Bioinformatics

    Bioinformatics 36 (3), 922-924, 2019-08-09

    Oxford University Press (OUP)

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