ArticleBioinformatics (Oxford, England)2024
VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Comparative Genomics and Metabolomics of Domesticated, Pladienolide-ProducingJournal of natural products · 2026Article
- ChoCallate: a computational pipeline for consensus germline variant calling in genomic sequencing data.PeerJ · 2026Article
- A Fitness Burden Drives the Reversion of in vitro Acquired Doxycycline Resistance inInfection and drug resistance · 2026Article
- Article
- Genome-wide approaches to bacterial strain typing: a history and review of recent methodological advances.Current opinion in infectious diseases · 2025Review
- Case Report: Genetic evolution ofWellcome open research · 2025Article
- ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing.BMC bioinformatics · 2024Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
motivationGenomic variations comprise a spectrum of alterations, ranging from single nucleotide polymorphisms (SNPs) to large-scale structural variants (SVs), which play crucial roles in bacterial evolution and species diversification. Accurately identifying SNPs and SVs is beneficial for subsequent evolutionary and epidemiological studies. This study presents VariantDetective (VD), a novel, user-friendly, and all-in-one pipeline combining SNP and SV calling to generate consensus genomic variants using multiple tools.
resultsThe VD pipeline accepts various file types as input to initiate SNP and/or SV calling, and benchmarking results demonstrate VD's robustness and high accuracy across multiple tested datasets when compared to existing variant calling approaches. AVAILABILITY AND IMPLEMENTATION: The source code, test data, and relevant information for VD are freely accessible at https://github.com/OLF-Bioinformatics/VariantDetective under the MIT License.
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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.