Article

Integer programming framework for pangenome-based genome inference

2024-10-29

Abstract excerpt

Affordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference genome is unreliable in highly polymorphic and repetitive regions, further impacting genotyping performance. Recent works highlight the advantage of haplotype-resolved pangeno...

Topics

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

Identifiers and source

Literature Corpus work: 3abe20c7-deb9-5b06-8641-cc6fe4f1814c
DOI: 10.1101/2024.10.27.620212

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Integer programming framework for pangenome-based genome inferenceDOI 10.1101/2024.10.27.620212Read

Pangenome-based genome inference using integer programming.Semantic proximity Read

Haplotype-aware sequence alignment to pangenome graphsSemantic proximity Read

Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes.Semantic proximity Read

Graphtyper: Population-scale genotyping using pangenome graphsSemantic proximity Read

Graphtyper enables population-scale genotyping using pangenome graphs.Semantic proximity Read

KAGE: fast alignment-free graph-based genotyping of SNPs and short indels.Semantic proximity Read

Investigating the topological motifs of inversions in pangenome graphsSemantic proximity Read

Fast and Accurate Genomic Analyses using Genome GraphsSemantic 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

Pangenome graph construction from genome alignments with Minigraph-Cactus.Semantic proximity Read

Pangenome Graph Construction from Genome Alignment with Minigraph-CactusSemantic proximity Read