Triti-Map is a Snakemake-based pipeline for gene mapping in Triticeae, which contains a suite of user-friendly computational packages and web-interface integrating multi-omics data from Triticeae species including genomic, epigenomic, evolutionary and homologous information.

Triti-Map could efficiently explore trait-related genes or functional elements not present in the reference genome and reduce the time and labor required for gene mapping in large genome species.

Triti-Map including three analysis modules:

• Interval Mapping Module
• Assembly Module
• Web-based Annotation Module

Interval Mapping Module and Assembly Module are command-line software. The input is mixed pool sequencing DNA-Seq(ChIP-Seq/WGS) or RNA-Seq data, which can be generated in one step including trait correlation genomic interval, mutation sites and new genes.

Web-based Annotation Module is an online analysis platform. We collected genomic information from each species of the Triticeae and hexaploid wheat varieties that have been sequenced. Gene function annotation and transcription factor binding site prediction are uniformly performed, while representative histone modification data of each species are integrated. The platform can perform various analyses, including SNP annotation and visualization, homologous gene analysis, Triticeae collinearity analysis, and new sequence function annotation, providing richer reference information for wheat family gene cloning.

Triti-Map optimization steps to address specific challenges of Triticeae gene-mapping

Author information

Developer: Fei Zhao(zhaofei920810@gmail.com)

Lab web page: http://bioinfo.cemps.ac.cn/zhanglab/