ArticleGenome biology2023
SPUMONI 2: improved classification using a pangenome index of minimizer digests.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Movi 2: fast and space-efficient queries on pangenomes.Bioinformatics (Oxford, England) · 2026Article
- Building genomic data structures from compressed representations using prefix-free parsing.Genome research · 2026Review
- Minimizing reference bias with an imputed personalized reference.Genome research · 2026Article
- Prefix-free parsing for merging big BWTs.International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium) · 2026Article
- KeBaB:International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium) · 2026Article
- Col-BWT: Pangenomic Seed Chaining with Maximal Matches Improves Read Classification.Journal of computational biology : a journal of computational molecular cell biology · 2026Article
- Article
- Robust 16S rRNA classification based on a compressed LCA index.Genome research · 2025Article
- SAFARI: pangenome alignment of ancient DNA using purine/pyrimidine encodings.NAR genomics and bioinformatics · 2025Article
- Columba: fast approximate pattern matching with optimized search schemes.Bioinformatics (Oxford, England) · 2025Article
- Movi 2: Fast and Space-Efficient Queries on Pangenomes.bioRxiv : the preprint server for biology · 2025Article
- SKiM: accurately classifying metagenomic ONT reads in limited memory.Bioinformatics (Oxford, England) · 2025Article
- b-move: faster lossless approximate pattern matching in a run-length compressed index.Algorithms for molecular biology : AMB · 2025Article
- Fast and flexible minimizer digestion with digest.Bioinformatics (Oxford, England) · 2025Article
- Mumemto: efficient maximal matching across pangenomes.Genome biology · 2025Article
- Mem-based pangenome indexing for k-mer queries.Algorithms for molecular biology : AMB · 2025Article
- Faster run-length compressed suffix arrays.Oasics : openaccess series in informatics · 2025Article
- An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025Article
- K2R: Tinted de Bruijn graphs implementation for efficient read extraction from sequencing datasets.Bioinformatics advances · 2025Article
- Movi Color: fast and accurate taxonomic classification with the move structure.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2025Article
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5 authors.
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Abstract
Genomics analyses use large reference sequence collections, like pangenomes or taxonomic databases. SPUMONI 2 is an efficient tool for sequence classification of both short and long reads. It performs multi-class classification using a novel sampled document array. By incorporating minimizers, SPUMONI 2's index is 65 times smaller than minimap2's for a mock community pangenome. SPUMONI 2 achieves a speed improvement of 3-fold compared to SPUMONI and 15-fold compared to minimap2. We show SPUMONI 2 achieves an advantageous mix of accuracy and efficiency in practical scenarios such as adaptive sampling, contamination detection and multi-class metagenomics classification.
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