ArticleiScience2019
MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants.
Article in iScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- A k-mer-based estimator of the substitution rate between repetitive sequences.Algorithms for molecular biology : AMB · 2026Article
- A scalable distributed pipeline for reference-free variants calling.BMC genomics · 2025Article
- Reference-Free Variant Calling with Local Graph Construction with ska lo (SKA).Molecular biology and evolution · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025Article
- Effects of spaced k-mers on alignment-free genotyping.Bioinformatics (Oxford, England) · 2023Article
- Pangenomic genotyping with the marker array.Algorithms for molecular biology : AMB · 2023Article
- SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads.Nature methods · 2023Article
- KAGE: fast alignment-free graph-based genotyping of SNPs and short indels.Genome biology · 2022Article
- Pangenomic Genotyping with the Marker Array.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2022Article
- MALVIRUS: an integrated application for viral variant analysis.BMC bioinformatics · 2022Article
- Computational graph pangenomics: a tutorial on data structures and their applications.Natural computing · 2022Article
- The Statistics ofJournal of computational biology : a journal of computational molecular cell biology · 2022Article
- Hardware acceleration of genomics data analysis: challenges and opportunities.Bioinformatics (Oxford, England) · 2021Article
- Disk compression of k-mer sets.Algorithms for molecular biology : AMB · 2021Article
- Nebula: ultra-efficient mapping-free structural variant genotyper.Nucleic acids research · 2021Article
- Shark: fishing relevant reads in an RNA-Seq sample.Bioinformatics (Oxford, England) · 2021Article
- Comparative genome analysis using sample-specific string detection in accurate long reads.Bioinformatics advances · 2021Article
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The amount of genetic variation discovered in human populations is growing rapidly leading to challenging computational tasks, such as variant calling. Standard methods for addressing this problem include read mapping, a computationally expensive procedure; thus, mapping-free tools have been proposed in recent years. These tools focus on isolated, biallelic SNPs, providing limited support for multi-allelic SNPs and short insertions and deletions of nucleotides (indels). Here we introduce MALVA, a mapping-free method to genotype an individual from a sample of reads. MALVA is the first mapping-free tool able to genotype multi-allelic SNPs and indels, even in high-density genomic regions, and to effectively handle a huge number of variants. MALVA requires one order of magnitude less time to genotype a donor than alignment-based pipelines, providing similar accuracy. Remarkably, on indels, MALVA provides even better results than the most widely adopted variant discovery tools.
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