ArticleGenome biology2020
GraphAligner: rapid and versatile sequence-to-graph alignment.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 136 papers.
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Who cites it
136 citing papers in PubMed, 270 citations in OpenAlex.
- An Icelandic pangenome reference.Nature · 2026Article
- Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.NAR genomics and bioinformatics · 2026Article
- Theseus: fast and optimal affine-gap sequence-to-graph alignment.Bioinformatics (Oxford, England) · 2026Article
- Telomere-to-telomere genome assembly and a pangenome for the rat.Cell genomics · 2026Article
- Automatic generation of model sequences for complex regions in assembly graphs with TTT.Cell genomics · 2026Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.Cell genomics · 2026Article
- A complete genome for the common marmoset.Cell · 2026Article
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- gaftools: a toolkit for analyzing and manipulating pangenome alignments.Bioinformatics (Oxford, England) · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- GBZ-base and GAF-base: Indexed pangenome file formats.bioRxiv : the preprint server for biology · 2026Article
- De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping.Briefings in bioinformatics · 2026Article
- Pangenome-based human genome analysis improves trait association and genomic prediction.bioRxiv : the preprint server for biology · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Lossless pangenome indexing using tag arrays.Algorithms for molecular biology : AMB · 2026Article
- MGA: a tool for haplotype-mixed assembly of long and accurate reads.Genome biology · 2026Article
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- Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.Nature communications · 2026Article
76 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome graphs can represent genetic variation and sequence uncertainty. Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pangenome graph. Yet, so far, this step is often prohibitively slow. We present GraphAligner, a tool for aligning long reads to genome graphs. Compared to the state-of-the-art tools, GraphAligner is 13x faster and uses 3x less memory. When employing GraphAligner for error correction, we find it to be more than twice as accurate and over 12x faster than extant tools.Availability: Package manager: https://anaconda.org/bioconda/graphaligner and source code: https://github.com/maickrau/GraphAligner.
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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.