ArticleGigaScience2022
MBGC: Multiple Bacteria Genome Compressor.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 19 citations in OpenAlex.
- Article
- MBGC2: Boosting compression via efficient encoding of approximate matches in genome collections.GigaScience · 2026Article
- Efficient and robust search of microbial genomes via phylogenetic compression.Nature methods · 2025Article
- JARVIS3: an efficient encoder for genomic data.Bioinformatics (Oxford, England) · 2024Article
- Compression rates of microbial genomes are associated with genome size and base composition.Genomics & informatics · 2024Article
- Article
- AGC: compact representation of assembled genomes with fast queries and updates.Bioinformatics (Oxford, England) · 2023Article
- AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data.GigaScience · 2022Article
- Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format.Patterns (New York, N.Y.) · 2022Review
- The complexity landscape of viral genomes.GigaScience · 2022Article
- MBGC: Multiple Bacteria Genome Compressor.GigaScience · 2022Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenomes within the same species reveal large similarity, exploited by specialized multiple genome compressors. The existing algorithms and tools are however targeted at large, e.g., mammalian, genomes, and their performance on bacteria strains is rather moderate.
resultsIn this work, we propose MBGC, a specialized genome compressor making use of specific redundancy of bacterial genomes. Its characteristic features are finding both direct and reverse-complemented LZ-matches, as well as a careful management of a reference buffer in a multi-threaded implementation. Our tool is not only compression efficient but also fast. On a collection of 168,311 bacterial genomes, totalling 587 GB, we achieve a compression ratio of approximately a factor of 1,265 and compression (respectively decompression) speed of ∼1,580 MB/s (respectively 780 MB/s) using 8 hardware threads, on a computer with a 14-core/28-thread CPU and a fast SSD, being almost 3 times more succinct and >6 times faster in the compression than the next best competitor.
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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.