Journal
MOLECULAR ECOLOGY RESOURCES
Volume 13, Issue 3, Pages 403-416Publisher
WILEY
DOI: 10.1111/1755-0998.12077
Keywords
annotation; de novo assembly; suture zones; transcriptomes; variant discovery
Funding
- National Science Foundation
- Museum of Vertebrate Zoology Wolff Fund
- Society of the Study of Evolution
Ask authors/readers for more resources
High-throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still poses notable challenges, especially for those working with organisms without a high-quality reference genome. For every stage of analysis from assembly to annotation to variant discovery researchers have to distinguish technical artefacts from the biological realities of their data before they can make inference. In this work, I explore these challenges by generating a large de novo comparative transcriptomic data set data for a clade of lizards and constructing a pipeline to analyse these data. Then, using a combination of novel metrics and an externally validated variant data set, I test the efficacy of my approach, identify areas of improvement, and propose ways to minimize these errors. I find that with careful data curation, HTS can be a powerful tool for generating genomic data for non-model organisms.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available