ArticleG3 (Bethesda, Md.)2023
Whole Animal Genome Sequencing: user-friendly, rapid, containerized pipelines for processing, variant discovery, and annotation of short-read whole genome sequencing data.
Article in G3 (Bethesda, Md.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed.
- A Comprehensive Analysis of the Agreement and Performance of Variant Annotation Programs in Equine Genomes.Genes · 2026Article
- ABCA12 Frameshift Deletion in Domestic Cats With Ichthyosis Fetalis.Veterinary dermatology · 2026Article
- Identification of an F13A1 frameshift variant associated with factor XIII deficiency in a Coonhound dog with severe coagulopathy.Journal of veterinary internal medicine · 2026Article
- Progressive abnormal gait in an adult Jack Russell Terrier with a homozygous frameshift variant in SETX (senataxin).Journal of veterinary internal medicine · 2026Article
- Myopathy due to a creatine deficiency disorder in a family of mixed breed dogs with a glycine amidinotransferase gene mutation.Journal of veterinary internal medicine · 2026Article
- Autoimmune lymphoproliferative syndrome in Boerboel dogs: clinicopathologic, diagnostic, and genetic characterization.Journal of veterinary internal medicine · 2026Article
- Germline Pathogenic Variant in the APC Gene Suggestive of Gardner Syndrome in a Pony.Case reports in veterinary medicine · 2026Article
- Identification of genetic variants associated with ear length in drop-eared dogs.Scientific reports · 2025Article
- Dystrophin-Deficient Muscular Dystrophy in a Family of Shiba Inu Dogs with a Complex Deletion EncompassingGenes · 2025Article
- Identification of a NovelGenes · 2025Article
- Unraveling the genetics of feline hypertrophic cardiomyopathy: a multiomics study of 138 cats.G3 (Bethesda, Md.) · 2025Article
- Establishing a robust genetic sequencing and gene expression data library in cardiovascularly healthy cats.Scientific reports · 2025Article
- Biliverdinuria Caused by ExonicGenes · 2024Article
- Analyses of whole-genome sequences from 185 North American Thoroughbred horses, spanning 5 generations.Scientific reports · 2024Article
- Acquired dysfunction of CFTR underlies cystic fibrosis-like disease of the canine gallbladder.American journal of physiology. Gastrointestinal and liver physiology · 2024Article
- Large-scale genomic analysis of the domestic dog informs biological discovery.Genome research · 2024Review
- Multi-Allelic Mitochondrial DNA Deletions in an Adult Dog with Chronic Weakness, Exercise Intolerance and Lactic Acidemia.Animals : an open access journal from MDPI · 2024Article
- Predicted genetic burden and frequency of phenotype-associated variants in the horse.Scientific reports · 2024Article
- A NovelJournal of fungi (Basel, Switzerland) · 2024Article
- Variants inAnimals : an open access journal from MDPI · 2024Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Advancements in massively parallel short-read sequencing technologies and the associated decreasing costs have led to large and diverse variant discovery efforts across species. However, processing high-throughput short-read sequencing data can be challenging with potential pitfalls and bioinformatics bottlenecks in generating reproducible results. Although a number of pipelines exist that address these challenges, these are often geared toward human or traditional model organism species and can be difficult to configure across institutions. Whole Animal Genome Sequencing (WAGS) is an open-source set of user-friendly, containerized pipelines designed to simplify the process of identifying germline short (SNP and indel) and structural variants (SVs) geared toward the veterinary community but adaptable to any species with a suitable reference genome. We present a description of the pipelines [adapted from the best practices of the Genome Analysis Toolkit (GATK)], along with benchmarking data from both the preprocessing and joint genotyping steps, consistent with a typical user workflow.
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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.