ArticleAlgorithms for molecular biology : AMB2023
Pangenomic genotyping with the marker array.
Article in Algorithms for molecular biology : AMB, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Minimizing reference bias with an imputed personalized reference.Genome research · 2026Article
- Robust 16S rRNA classification based on a compressed LCA index.Genome research · 2025Article
- Pangenome-based genome inference using integer programming.Genome research · 2025Article
- Integer programming framework for pangenome-based genome inference.bioRxiv : the preprint server for biology · 2024Article
- Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference.Life (Basel, Switzerland) · 2023Review
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Authors and funding
3 authors.
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Abstract
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/alshai/rowbowt .
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