ArticleiScience2020
Scalable Pairwise Whole-Genome Homology Mapping of Long Genomes with BubbZ.
Article in iScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn GraphsJournal of computational biology : a journal of computational molecular cell biology · 2024Article
- Graphite: painting genomes using a colored de Bruijn graph.NAR genomics and bioinformatics · 2024Article
- Revisiting the complexity of and algorithms for the graph traversal edit distance and its variants.Algorithms for molecular biology : AMB · 2024Article
- Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2.Genome biology · 2022Article
- Multiple genome alignment in the telomere-to-telomere assembly era.Genome biology · 2022Review
- The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance.Bioinformatics (Oxford, England) · 2022Article
- Review
- Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections.Bioinformatics (Oxford, England) · 2021Article
- Review
Corrections and comments
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Authors and funding
2 authors.
Funding
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Abstract
Pairwise whole-genome homology mapping is the problem of finding all pairs of homologous intervals between a pair of genomes. As the number of available whole genomes has been rising dramatically in the last few years, there has been a need for more scalable homology mappers. In this paper, we develop an algorithm (BubbZ) for computing whole-genome pairwise homology mappings, especially in the context of all-to-all comparison for multiple genomes. BubbZ is based on an algorithm for computing chains in compacted de Bruijn graphs. We evaluate BubbZ on simulated datasets, a dataset composed of 16 long mouse genomes, and a large dataset of 1,600 Salmonella genomes. We show up to approximately an order of magnitude speed improvement, compared with MashMap2 and Minimap2, while retaining similar accuracy.
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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.