ArticleGenome biology2021
Gramtools enables multiscale variation analysis with genome graphs.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 35 citations in OpenAlex.
- Minimizing reference bias with an imputed personalized reference.Genome research · 2026Article
- Benchmarking within-sample minority variant detection with short-read sequencing inbioRxiv : the preprint server for biology · 2026Article
- Module-level recombination drives DBLMSP polymorphism and functional conservation in Plasmodium falciparum.Parasite (Paris, France) · 2026Article
- Pangenome-based genome inference using integer programming.Genome research · 2025Article
- Distribution and Genotypic Landscape of Tick-Borne Encephalitis Virus in Ticks from Latvia from 2019 to 2023.Pathogens (Basel, Switzerland) · 2025Article
- Review
- PangeBlocks: customized construction of pangenome graphs via maximal blocks.BMC bioinformatics · 2024Article
- Integer programming framework for pangenome-based genome inference.bioRxiv : the preprint server for biology · 2024Article
- Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References.Annual review of genomics and human genetics · 2024Review
- A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline.Genome biology · 2024Article
- Role for gene conversion in the evolution of cell-surface antigens of the malaria parasite Plasmodium falciparum.PLoS biology · 2024Article
- Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data.GigaScience · 2024Article
- Drug resistance prediction forMicrobial genomics · 2023Article
- Article
- Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes.Genome biology · 2022Article
- The 2021 WHO catalogue ofThe Lancet. Microbe · 2022Article
- Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel.Genome biology · 2022Article
- Population-scale genotyping of structural variation in the era of long-read sequencing.Computational and structural biotechnology journal · 2022Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Genome graphs allow very general representations of genetic variation; depending on the model and implementation, variation at different length-scales (single nucleotide polymorphisms (SNPs), structural variants) and on different sequence backgrounds can be incorporated with different levels of transparency. We implement a model which handles this multiscale variation and develop a JSON extension of VCF (jVCF) allowing for variant calls on multiple references, both implemented in our software gramtools. We find gramtools outperforms existing methods for genotyping SNPs overlapping large deletions in M. tuberculosis and is able to genotype on multiple alternate backgrounds in P. falciparum, revealing previously hidden recombination.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.