ArticleProceedings. Data Compression Conference2021
PHONI: Streamed Matching Statistics with Multi-Genome References.
Article in Proceedings. Data Compression Conference, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Building genomic data structures from compressed representations using prefix-free parsing.Genome research · 2026Review
- Bounding the Average Move Structure Query for Faster and Smaller RLBWT Permutations.LIPIcs : Leibniz international proceedings in informatics · 2026Article
- Suffixient Arrays: A New Efficient Suffix Array Compression Technique.Theory of computing systems · 2026Article
- Article
- Columba: fast approximate pattern matching with optimized search schemes.Bioinformatics (Oxford, England) · 2025Article
- b-move: faster lossless approximate pattern matching in a run-length compressed index.Algorithms for molecular biology : AMB · 2025Article
- Generating multiple alignments on a pangenomic scale.Bioinformatics (Oxford, England) · 2025Article
- Sigmoni: classification of nanopore signal with a compressed pangenome index.Bioinformatics (Oxford, England) · 2024Article
- b-move: faster bidirectional character extensions in a run-length compressed index.bioRxiv : the preprint server for biology · 2024Article
- Sigmoni: classification of nanopore signal with a compressed pangenome index.bioRxiv : the preprint server for biology · 2023Article
- Augmented Thresholds for MONI.Proceedings. Data Compression Conference · 2023Article
- An Upper Bound and Linear-Space Queries on the LZ-End Parsing.Proceedings of the ... Annual ACM-SIAM Symposium on Discrete Algorithms. ACM-SIAM Symposium on Discrete Algorithms · 2022Article
- Fast and Space-Efficient Construction of AVL Grammars from the LZ77 Parsing.LIPIcs : Leibniz international proceedings in informatics · 2021Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this case, which Rossi et al. recently implemented, but it uses two passes over the patterns and buffers a pointer for each character during the first pass. In this paper, we simplify their solution and make it streaming, at the cost of slowing it down slightly. This means that, first, we can compute the matching statistics of several long patterns (such as whole human chromosomes) in parallel while still using a reasonable amount of RAM; second, we can compute matching statistics online with low latency and thus quickly recognize when a pattern becomes incompressible relative to the database. Our code is available at https://github.com/koeppl/phoni.
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Registered trials
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