ArticleBioinformatics (Oxford, England)2024
BWT construction and search at the terabase scale.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Efficient sequence alignment against millions of prokaryotic genomes with LexicMap.Nature biotechnology · 2026Article
- New algorithm enables fast 'gold-standard' search of the world's largest microbial DNA archives.Nature biotechnology · 2026Article
- AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics.bioRxiv : the preprint server for biology · 2026Article
- Movi 2: fast and space-efficient queries on pangenomes.Bioinformatics (Oxford, England) · 2026Article
- RLBWT-based LCP computation in compressed space for terabase-scale pangenome analysis.Bioinformatics (Oxford, England) · 2026Article
- Lossless pangenome indexing using tag arrays.Algorithms for molecular biology : AMB · 2026Article
- Finding low-complexity DNA sequences with longdust.Bioinformatics (Oxford, England) · 2026Article
- RLBWT-Based LCP Computation in Compressed Space for Terabase-Scale Pangenome Analysis.bioRxiv : the preprint server for biology · 2026Article
- Lossless Pangenome Indexing Using Tag Arrays.Research square · 2026Article
- Prefix-free parsing for merging big BWTs.International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium) · 2026Article
- An Efficient Dynamic Data Structure for Haplotype Matching and Compression on Biobank-Scale Data.Journal of computational biology : a journal of computational molecular cell biology · 2026Article
- FroM Superstring to Indexing: a space-efficient index for unconstrainedBioinformatics advances · 2026Article
- KeBaB:International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium) · 2026Article
- Article
- Columba: fast approximate pattern matching with optimized search schemes.Bioinformatics (Oxford, England) · 2025Article
- Article
- Movi 2: Fast and Space-Efficient Queries on Pangenomes.bioRxiv : the preprint server for biology · 2025Article
- Mumemto: efficient maximal matching across pangenomes.Genome biology · 2025Article
- DynamicbioRxiv : the preprint server for biology · 2025Article
- Haplotype Matching with GBWT for Pangenome Graphs.bioRxiv : the preprint server for biology · 2025Article
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Abstract
motivationBurrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction is resource intensive and hard to be parallelized, and many methods for querying large full-text indices only report exact matches or their simple extensions. These limitations have hampered the biological applications of full-text indices.
resultsWe developed ropebwt3 for efficient BWT construction and query. Ropebwt3 indexed 320 assembled human genomes in 65 h and indexed 7.3 terabases of commonly studied bacterial assemblies in 26 days. This was achieved using up to 170 gigabytes of memory at the peak without working disk space. Ropebwt3 can find maximal exact matches and inexact alignments under affine-gap penalties, and can retrieve similar local haplotypes matching a query sequence. It demonstrates the feasibility of full-text indexing at the terabase scale. AVAILABILITY AND IMPLEMENTATION: https://github.com/lh3/ropebwt3.
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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.