MsPAC: a tool for haplotype-phased structural variant detection | Zendy

Oscar L. Rodriguez | Zendy; Anna Ritz | Zendy; Andrew J. Sharp | Zendy; Ali Bashir | Zendy

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MsPAC: a tool for haplotype-phased structural variant detection

Author(s) -

Oscar L. Rodriguez,

Anna Ritz,

Andrew J. Sharp,

Ali Bashir

Publication year - 2019

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btz618

Subject(s) - haplotype , genome , genomics , sequence assembly , dna sequencing , computer science , software , computational biology , 1000 genomes project , biology , genetics , gene , genotype , gene expression , transcriptome , single nucleotide polymorphism , programming language

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.

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