MAPtools

MAPtools analyzes genomic data from bulked segregant analysis experiments, including mapping-by-sequencing (MBS) and quantitative trait locus sequencing (QTL-seq) experiments, by calculating allele count-based statistics, generating plots, and annotating mutation effects.

Key Features:

• Allele Count-Based Statistics: MAPtools calculates allele count-based statistics for bulked segregant analysis experiments.
• Plot Generation: MAPtools generates plots to pinpoint candidate regions in MBS and QTL-seq experiments.
• Mutation Effect Annotation: MAPtools annotates the effects of SNP and indel mutations.

Scientific Applications:

• Mapping-by-Sequencing (MBS): MAPtools analyzes genomic data from MBS experiments to identify genes underlying traits.
• QTL-Seq Analysis: MAPtools analyzes genomic data from quantitative trait locus sequencing experiments for agronomic trait mapping.
• Candidate Region Identification: MAPtools generates plots to pinpoint genomic regions associated with traits of interest in mapping populations.

Methodology:

MAPtools is implemented as an open-source Python3 application providing command-line tools for analysis and visualization.