/WheatPangenome

Custom code developed for WheatPangenome Project.

Primary LanguageShellMIT LicenseMIT

WheatPangenome

This repo contains customized codes used in WheatPangenome project. Codes are grouped into multiple folders according to their usage. Appropriate comments and user manuals have been added within these scripts. A README file is provided including the descriptions of each folder.

System requirements

  • Bedtools (v2.27.1)
  • NLR-Annotator (v2.1)
  • RepeatMasker (v4.0.7)
  • Datamash (v1.4)
  • NGenomeSyn (v1.1.2)
  • Minimap2 (v2.22)
  • R (v3.6)

Installation guide

All softwares listed in system requirements could be downloaded and installed following instructions on their offical websites.

Demos and corresponding instructions

Demos and corresponding instructions are in each foler.Demos and corresponding instructions are in each foler.

Brief description of code in each folder

  1. NLR:
    Detecting NLR genes from wheat accessions using NLR-Annotator.
  2. CopyNumber:
    Counting copy number of VRN-A1 from wheat accessions using NGenomeSyn.
  3. Subtelomere:
    Detecting subtelomere regions from wheat accessions using RepeatMasker.
  4. NGenomeSyn:
    Detecting and visualizing the syntenic blocks between wheat accessions using NGenomeSyn.