Article

Sequence variation aware genome references and read mapping with the variation graph toolkit

2017-12-15

Abstract excerpt

Reference genomes guide our interpretation of DNA sequence data. However, conventional linear references are fundamentally limited in that they represent only one version of each locus, whereas the population may contain multiple variants. When the reference represents an individual’s genome poorly, it can impact read mapping and introduce bias. Variation graphs are bidirected DNA sequence graphs that compactly re...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 36a924f4-5166-5a14-9923-f81e68ecbde1
DOI: 10.1101/234856

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Sequence variation aware genome references and read mapping with the variation graph toolkitDOI 10.1101/234856Read

Fast and Accurate Genomic Analyses using Genome GraphsSemantic proximity Read

Genome GraphsSemantic proximity Read

Fast alignment of reads to a variation graph with application to SNP detection.Semantic proximity Read

Population-specific genome graphs improve high-throughput sequencing data analysis: A case study on the Pan-African genomeSemantic proximity Read

Defining and cataloging variants in pangenome graphsSemantic proximity Read

SVarp: pangenome-based structural variant discoverySemantic proximity Read

Personalized pangenome references.Semantic proximity Read

Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkitSemantic proximity Read

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg GiraffeSemantic proximity Read

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg GiraffeSemantic proximity Read

PanVariants: Best Practice for Pangenome-based Variant Calling Pipeline and FrameworkSemantic proximity Read

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graphSemantic proximity Read