Whole Animal Genome Sequencing: user-friendly, rapid, containerized pipelines for processing, variant discovery, and annotation of short-read whole genome sequencing data

Jonah N. Cullen, Steven G. Friedenberg

Research output: Contribution to journalArticlepeer-review

10 Scopus citations

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.

Original languageEnglish (US)
Article numberjkad117
JournalG3: Genes, Genomes, Genetics
Volume13
Issue number8
DOIs
StatePublished - Aug 2023

Bibliographical note

Funding Information:
JNC was funded by a United States Department of Agriculture National Institute of Food and Agriculture Predoctoral Fellowship as part of the Agriculture and Food Research Initiative (https://nifa.usda.gov/) (2020-67034-31739). SGF is supported in part by an NIH Special Emphasis Research Career Award (K01 OD027058) in Pathology and Comparative Medicine sponsored by the Division of Comparative Medicine, Office of Research Infrastructure Programs.

Publisher Copyright:
© The Author(s) 2023.

Keywords

  • pipeline
  • variants
  • whole genome sequencing

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

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