Plant.annot

Repository for the annotation pipeline used @ PGSB. Tested on plant genomes.

Requirements

Most dependencies should be covered by the provided conda environment

Usage

• install anaconda from anaconda.org
• install bioconda (see bioconda)
• clone repository

git clone https://github.com/PGSB-HMGU/plant.annot.git

• cd into plant.annot directory

cd plant.annot

• create plant.annot environment using the provided yaml file

conda env create --file=plant.annot.yaml

• activate environment

conda activate plant.annot

• download and install Transdecoder 3.0.1 from Transdecoder
• download transposon database PTREP from Hypothetical TREP protein sequences
• download reference proteins from uniprot
• download reference proteins form closely related species
• protein sequences must include STOP amino acids as ('*')
• build hisat2 index
• build gmap index
• split large chromosomes into single files to speed up gth
• edit config.yaml
  • define ISOseq data as described in config.yaml
  • define reference proteins as described in config.yaml
  • define RNAseq data as described in config.yaml
  • review executable section in config.yaml
• perform a dry run

snakemake final_files -np

• run locally

snakemake final_files --cores cores

• run on a cluster

snakemake final_files --cluster "qsub"