ReviewFrontiers in genetics2015
Best practices for evaluating single nucleotide variant calling methods for microbial genomics.
Review in Frontiers in genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers, 1 of them a synthesis that pooled it.
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Who cites it
101 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Surveillance of antibiotic-resistant bacteria integrating whole genome sequencing and epidemiological information - a global, systematic review, 2012-2023.Antimicrobial resistance and infection control · 2026Pooled it
- Growth Phase-Related DNA Methylation and Localized DNA Fragment Density Variation inEpigenomes · 2026Article
- Fifteen Years of the Genome Analysis Toolkit as the De Facto Standard in Short-Read Variant Calling.International journal of molecular sciences · 2026Review
- Benchmarking Illumina and Oxford Nanopore Technologies (ONT) sequencing platforms for whole genome sequencing of bacterial genomes and use in clinical microbiology.BMC medical genomics · 2026Article
- Article
- An ANIr-based methodology to determine if two sequence-discrete populations are identical and identify cosmopolitan prokaryotic populations.ISME communications · 2026Article
- A comparison of short- and long-read whole-genome sequencing for microbial pathogen epidemiology.mSystems · 2025Article
- Design of a Prospective Human-Animal Cohort Study to Evaluate the Role of Camels and Other Livestock Species in the Transmission ofInternational journal of environmental research and public health · 2025Article
- The genomic diversity and spatial patterns of Mycobacterium bovis in Ireland revealed by whole genome sequencing.Irish veterinary journal · 2025Article
- A comparison of short- and long-read whole genome sequencing for microbial pathogen epidemiology.bioRxiv : the preprint server for biology · 2025Article
- Characterization of Novel Luteoviruses in Canadian Highbush Blueberries Using High-Throughput Sequencing.Viruses · 2025Article
- MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples.Bioinformatics (Oxford, England) · 2025Article
- A reproducible ddRAD-seq protocol reveals novel genomic association signatures for fruit-related traits in peach.Plant methods · 2025Article
- Genomic and Pangenomic Insights intoPathogens (Basel, Switzerland) · 2025Article
- Discovery of variation in genes related to agronomic traits by sequencing the genome of Cucurbita pepo varieties.BMC genomics · 2025Article
- NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction.PLoS computational biology · 2025Article
- Does strain-level persistence of lactobacilli in long-term back-slopped sourdoughs inform on domestication of food-fermenting lactic acid bacteria?Applied and environmental microbiology · 2024Article
- First draft reference genome and annotation of the alternative oil species Physaria fendleri.G3 (Bethesda, Md.) · 2024Article
- Exploring the impact of sequence context on errors in SNP genotype calling with whole genome sequencing data using AI-based autoencoder approach.NAR genomics and bioinformatics · 2024Article
- Phase variable colony variants are conserved acrossmSphere · 2024Article
41 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Innovations in sequencing technologies have allowed biologists to make incredible advances in understanding biological systems. As experience grows, researchers increasingly recognize that analyzing the wealth of data provided by these new sequencing platforms requires careful attention to detail for robust results. Thus far, much of the scientific Communit's focus for use in bacterial genomics has been on evaluating genome assembly algorithms and rigorously validating assembly program performance. Missing, however, is a focus on critical evaluation of variant callers for these genomes. Variant calling is essential for comparative genomics as it yields insights into nucleotide-level organismal differences. Variant calling is a multistep process with a host of potential error sources that may lead to incorrect variant calls. Identifying and resolving these incorrect calls is critical for bacterial genomics to advance. The goal of this review is to provide guidance on validating algorithms and pipelines used in variant calling for bacterial genomics. First, we will provide an overview of the variant calling procedures and the potential sources of error associated with the methods. We will then identify appropriate datasets for use in evaluating algorithms and describe statistical methods for evaluating algorithm performance. As variant calling moves from basic research to the applied setting, standardized methods for performance evaluation and reporting are required; it is our hope that this review provides the groundwork for the development of these standards.
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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.