AFIG v0.1.0

Using BUSCO Lineage data to train HMM model and annotate fungi genome.
By using e2e to identify the lineage of your fungi genome. This script will automatically find a busco dataset and map conserved ancestral proteins to this genome. SNAP will be used to train a species-specific HMM to annotate your genome. This pipeline will also configure a bash script for further antiSMASH analysis.

Requirements

Maker v3.01
snap
e2e

Install

pip install e2e
git clone https://github.com/JinyuanSun/AFIG.git
cd AFIG && tar vxzf fungi_busco_sub.tar.gz && export PATH="$(pwd):$PATH"

Usage

usage: genome_annotation_pipe.py [-h] [-n NAME] [-g GENOME_FILE_NAME] [-e ENGINE] [-p THREAD_NUM]

Automate, RNA-seq free, fungi genome annotation pipeline.

optional arguments:
  -h, --help            show this help message and exit
  -n NAME, --name NAME
  -g GENOME_FILE_NAME, --genome_file_name GENOME_FILE_NAME
  -e ENGINE, --engine ENGINE
                        use maker or exonerate
  -p THREAD_NUM, --thread_num THREAD_NUM

demo: genome_annotation_pipe.py -n Apiotrichum_mycotoxinovorans -g Am_genome.fasta -p 16 -e maker

Change Log

2021-11-23:
Built a sub-database of released official BUSCO databse. Only fungi are included.

2021-11-22:
Replace taxonkit with ETE Toolkit.
ETE is a Python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic trees.

To Do List

1. Find or make a better software to replace Maker. It is too heavy.

For further functional annotation and visulation, refer to CMPP.

Feel free to contact me or contribute to this open-source project to make it better!