ArticlePloS one2014
Indexes of large genome collections on a PC.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 16 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- MBGC2: Boosting compression via efficient encoding of approximate matches in genome collections.GigaScience · 2026Article
- MBGC: Multiple Bacteria Genome Compressor.GigaScience · 2022Article
- A variant selection framework for genome graphs.Bioinformatics (Oxford, England) · 2021Article
- Efficient Construction of a Complete Index for Pan-Genomics Read Alignment.Journal of computational biology : a journal of computational molecular cell biology · 2020Article
- Bit-parallel sequence-to-graph alignment.Bioinformatics (Oxford, England) · 2019Article
- Fully-sensitive seed finding in sequence graphs using a hybrid index.Bioinformatics (Oxford, England) · 2019Article
- Pattern Matching for DNA Sequencing Data Using Multiple Bloom Filters.BioMed research international · 2019Article
- FORGe: prioritizing variants for graph genomes.Genome biology · 2018Article
- Towards pan-genome read alignment to improve variation calling.BMC genomics · 2018Article
- Computational pan-genomics: status, promises and challenges.Briefings in bioinformatics · 2018Review
- The effects of sampling on the efficiency and accuracy of k-mer indexes: Theoretical and empirical comparisons using the human genome.PloS one · 2017Article
- Sequence Factorization with Multiple References.PloS one · 2015Article
- Indexing Arbitrary-Length k-Mers in Sequencing Reads.PloS one · 2015Article
- Article
- Searching and Indexing Genomic Databases via Kernelization.Frontiers in bioengineering and biotechnology · 2015Review
- Correction: Indexes of Large Genome Collections on a PC.PloS one · 2015Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The availability of thousands of individual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key operation useful in such analyses is aligning sequencing reads against a collection of genomes, which is costly with the use of existing algorithms due to their large memory requirements. We present MuGI, Multiple Genome Index, which reports all occurrences of a given pattern, in exact and approximate matching model, against a collection of thousand(s) genomes. Its unique feature is the small index size, which is customisable. It fits in a standard computer with 16-32 GB, or even 8 GB, of RAM, for the 1000GP collection of 1092 diploid human genomes. The solution is also fast. For example, the exact matching queries (of average length 150 bp) are handled in average time of 39 µs and with up to 3 mismatches in 373 µs on the test PC with the index size of 13.4 GB. For a smaller index, occupying 7.4 GB in memory, the respective times grow to 76 µs and 917 µs. Software is available at http://sun.aei.polsl.pl/mugi under a free license. Data S1 is available at PLOS One online.
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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.