High-performance pipeline for MutMap and QTL-seq

PeerJ

article

Yu Sugihara¹  Lester Young³  Hiroki Yaegashi¹  Satoshi Natsume¹  Daniel J. Shea¹  Hiroki Takagi⁴  Helen Booker³  Hideki Innan⁶  Ryohei Terauchi¹  Akira Abe¹ 

[1] Department of Genomics and Breeding, Iwate Biotechnology Research Center;Graduate School of Agriculture, Kyoto University;Department of Plant Sciences, University of Saskatchewan;Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University;Department of Plant Agriculture, University of Guelph;Graduate University for Advanced Studies

关键词: Bioinformatics;    Bulked-segregant analysis;    QTL analysis;    Mutation mapping;    Agricultural science;   

DOI  :  10.7717/peerj.13170

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

SummaryBulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify loci contributing to important phenotypic traits. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. These updated pipelines are approximately 5–8 times faster than the previous pipeline, are easier for novice users to use, and can be easily installed through bioconda with all dependencies.AvailabilityThe new pipelines of MutMap and QTL-seq are written in Python and can be installed via bioconda. The source code and manuals are available online (MutMap: https://github.com/YuSugihara/MutMap, QTL-seq: https://github.com/YuSugihara/QTL-seq).

【 授权许可】

CC BY