ArticleAlgorithms for molecular biology : AMB2019
SNPs detection by eBWT positional clustering.
Article in Algorithms for molecular biology : AMB, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- PISAD: reference-free intraspecies sample anomalies detection tool based on k-mer counting.GigaScience · 2025Article
- Identification and high-throughput genotyping of single nucleotide polymorphism markers in a non-model conifer (Abies nordmanniana (Steven) Spach).Scientific reports · 2023Article
- phyBWT2: phylogeny reconstruction via eBWT positional clustering.Algorithms for molecular biology : AMB · 2023Article
- MONI: A Pangenomic Index for Finding Maximal Exact Matches.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Computing the original eBWT faster, simpler, and with less memory.International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium) · 2021Article
- Detection of Single Nucleotide Polymorphisms by Fluorescence Embedded Dye SYBR Green I Based on Graphene Oxide.Frontiers in chemistry · 2021Article
- Variable-order reference-free variant discovery with the Burrows-Wheeler Transform.BMC bioinformatics · 2020Article
- BITS2019: the sixteenth annual meeting of the Italian society of bioinformatics.BMC bioinformatics · 2020Article
- Metagenomic analysis through the extended Burrows-Wheeler transform.BMC bioinformatics · 2020Article
- metaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics.PloS one · 2020Article
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Authors and funding
4 authors.
Funding
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Abstract
backgroundSequencing technologies keep on turning cheaper and faster, thus putting a growing pressure for data structures designed to efficiently store raw data, and possibly perform analysis therein. In this view, there is a growing interest in alignment-free and reference-free variants calling methods that only make use of (suitably indexed) raw reads data.
resultsWe develop the
conclusionsBased on the results of the experiments on synthetic and real data, we conclude that the positional clustering framework can be effectively used for the problem of identifying SNPs, and it appears to be a promising approach for calling other type of variants directly on raw sequencing data. AVAILABILITY: The software ebwt2snp is freely available for academic use at: https://github.com/nicolaprezza/ebwt2snp.
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