Discover Community Create You

Loading publication...

Noodle always counts identifier-free feature events for service operation. With your permission, Google Analytics can also estimate audience and engagement. Search text, publication identifiers, cookies, IP addresses and browser fingerprints are never included in Noodle's first-party event counters.

Privacy details

Article

A Cautionary Note on the Use of Genotype Callers in Phylogenomics.

Systematic biology - 16 Jun 2021

Duchen Pablo, Salamin Nicolas

Abstract excerpt

Next-generation-sequencing genotype callers are commonly used in studies to call variants from newly sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional genotype callers, such as the one from GATK, is that they are...

Read the complete abstract on PubMed

Topics

Share this publication in a Topic to start or enrich a Post.

Share to Genomics
Share to Genotype
Share to Genotyping Techniques

Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

Share to High-Throughput Nucleotide Sequencing

Share to Phylogeny

Share to Polymorphism, Single Nucleotide

Source

Open in PubMed Open full text

Identifiers

PMID: 33084875
DOI: 10.1093/sysbio/syaa081
PMCID: PMC8208803

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 6 Sept 2026. Manifest publication-graph-cohort-2026-09-06.1.

Source receipt: pubmed, retrieved 6 Sept 2026.

Related research

Semantic proximity does not establish scientific evidence.

Research trail→

Click a neighbor to travelStep 1 · 12 closest

A Cautionary Note on the Use of Genotype Callers in Phylogenomics.PMID 33084875Read ↗

Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology.Semantic proximity Read ↗

The Critical Role of Choosing Appropriate Genotype Caller and Reference Genome for Population Genomic Inference: A Demonstration Study with Five Pterocarya SpeciesSemantic proximity Read ↗

Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics.Semantic proximity Read ↗

PISAD: reference-free intraspecies sample anomalies detection tool based on k-mer counting.Semantic proximity Read ↗

Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects.Semantic proximity Read ↗

Generalizable characteristics of false-positive bacterial variant calls.Semantic proximity Read ↗

Genomic diversity affects the accuracy of bacterial SNP calling pipelinesSemantic proximity Read ↗

Estimating and accounting for genotyping errors in RAD-seq experiments.Semantic proximity Read ↗

Robust and efficient software for reference-free genomic diversity analysis of genotyping-by-sequencing data on diploid and polyploid species.Semantic proximity Read ↗

metaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics.Semantic proximity Read ↗

Pitfalls of genotyping microbial communities with rapidly growing genome collections.Semantic proximity Read ↗

Identifying species-specific k-mers for fast and accurate metagenotyping with Maast and GT-Pro.Semantic proximity Read ↗

⌁Select a neighboring publication to make it the new centre.