ArticleBioinformatics (Oxford, England)2023
AGC: compact representation of assembled genomes with fast queries and updates.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Personalized reference genome-based pipeline reveals comprehensive haplotype-resolved views of cancer genomes.bioRxiv : the preprint server for biology · 2026Article
- Navigating the pangenome coordinate system with Shredtools.bioRxiv : the preprint server for biology · 2026Article
- chewBBACA 3: lowering the barrier for scalable and detailed whole- and core-genome multilocus sequence typing.Genome medicine · 2026Article
- Compressive pangenomics using mutation-annotated networks.Nature genetics · 2026Article
- MBGC2: Boosting compression via efficient encoding of approximate matches in genome collections.GigaScience · 2026Article
- Loss of CFHR5 function reduces the risk for age-related macular degeneration.Nature communications · 2025Article
- Efficient and robust search of microbial genomes via phylogenetic compression.Nature methods · 2025Article
- JARVIS3: an efficient encoder for genomic data.Bioinformatics (Oxford, England) · 2024Article
- BWT construction and search at the terabase scale.Bioinformatics (Oxford, England) · 2024Article
- Complex genetic variation in nearly complete human genomes.bioRxiv : the preprint server for biology · 2024Article
- Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References.Annual review of genomics and human genetics · 2024Review
- Article
- Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes.Nature methods · 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
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Authors and funding
3 authors.
Funding
Abstract
motivationHigh-quality sequence assembly is the ultimate representation of complete genetic information of an individual. Several ongoing pangenome projects are producing collections of high-quality assemblies of various species. Each project has already generated assemblies of hundreds of gigabytes on disk, greatly impeding the distribution of and access to such rich datasets.
resultsHere, we show how to reduce the size of the sequenced genomes by 2-3 orders of magnitude. Our tool compresses the genomes significantly better than the existing programs and is much faster. Moreover, its unique feature is the ability to access any contig (or its part) in a fraction of a second and easily append new samples to the compressed collections. Thanks to this, AGC could be useful not only for backup or transfer purposes but also for routine analysis of pangenome sequences in common pipelines. With the rapidly reduced cost and improved accuracy of sequencing technologies, we anticipate more comprehensive pangenome projects with much larger sample sizes. AGC is likely to become a foundation tool to store, distribute and access pangenome data. AVAILABILITY AND IMPLEMENTATION: The source code of AGC is available at https://github.com/refresh-bio/agc. The package can be installed via Bioconda at https://anaconda.org/bioconda/agc. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.