Articles
Automating and documenting workflows for marker design from crop next-generation-sequencing data
Article number
1203_6
Pages
41 – 46
Language
English
Abstract
Next-generation-sequencing (NGS) technologies now enable researchers to readily survey genetic variation in any crop or context.
Although global genotyping is becoming routine, the targeted validation of selected variants for marker-aided selection (MAS) or other diagnostic applications remains challenging.
In this paper, we survey our experiences and strategies for automating PCR marker design in non-model crop genomes.
Recent enhancements in reproducible document authoring, software and environment management and genomic data programming have made the Python ecosystem well suited to the development of scalable toolkits for marker design.
Although global genotyping is becoming routine, the targeted validation of selected variants for marker-aided selection (MAS) or other diagnostic applications remains challenging.
In this paper, we survey our experiences and strategies for automating PCR marker design in non-model crop genomes.
Recent enhancements in reproducible document authoring, software and environment management and genomic data programming have made the Python ecosystem well suited to the development of scalable toolkits for marker design.
Authors
J. McCallum, M. Knäbel, E. Buck, H. Kong, T. Millar, B. Davis, S. Thomson, M. Pither‑Joyce, Z. Dwight, S. Baldwin
Keywords
genetic markers, genomics, programming
Online Articles (25)