ArticlePloS one2015
Indexing Arbitrary-Length k-Mers in Sequencing Reads.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 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.
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Who cites it
6 citing papers in PubMed.
- MBGC2: Boosting compression via efficient encoding of approximate matches in genome collections.GigaScience · 2026Article
- PgRC2: engineering the compression of sequencing reads.Bioinformatics (Oxford, England) · 2025Article
- A comprehensive evaluation of long read error correction methods.BMC genomics · 2020Review
- Variable-order reference-free variant discovery with the Burrows-Wheeler Transform.BMC bioinformatics · 2020Article
- SNPs detection by eBWT positional clustering.Algorithms for molecular biology : AMB · 2019Article
- Pattern Matching for DNA Sequencing Data Using Multiple Bloom Filters.BioMed research international · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating k-mers in sequencing reads. Our solution, PgSA (pseudogenome suffix array), based on finding overlapping reads, is competitive to the existing algorithms in the space use, query times, or both. The main applications of our index include variant calling, error correction and analysis of reads from RNA-seq experiments.
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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.