Author:
Martínez-Guardiola César,Parreño Ricardo,Candela Héctor
Abstract
Abstract
Background
Classical mutagenesis is a powerful tool that has allowed researchers to elucidate the molecular and genetic basis of a plethora of processes in many model species. The integration of these methods with modern massively parallel sequencing techniques, initially in model species but currently also in many crop species, is accelerating the identification of genes underlying a wide range of traits of agronomic interest.
Results
We have developed MAPtools, an open-source Python3 application designed specifically for the analysis of genomic data from bulked segregant analysis experiments, including mapping-by-sequencing (MBS) and quantitative trait locus sequencing (QTL-seq) experiments. We have extensively tested MAPtools using datasets published in recent literature.
Conclusions
MAPtools gives users the flexibility to customize their bioinformatics pipeline with various commands for calculating allele count-based statistics, generating plots to pinpoint candidate regions, and annotating the effects of SNP and indel mutations. While extensively tested with plants, the program is versatile and applicable to any species for which a mapping population can be generated and a sequenced genome is available.
Availability and implementation
MAPtools is available under GPL v3.0 license and documented as a Python3 package at https://github.com/hcandela/MAPtools.
Funder
Universidad Miguel Hernández
Publisher
Springer Science and Business Media LLC