Annotation Pipelines

This describes the **process** of 5 different **annotation pipelines** : **Prokka**, **MaGe**, **DFAST**, **RAST** and **IMG**

# 1. Annotation with Prokka (rapid prokaryotic genome annotation)
load right conda environment with the latest version of Prokka

    source $CONDA3/activate prokka-1.13
    mkdir filename
    prokka --addgenes -outdir assemblygenome.fasta

# 2. Annotation with MaGe (Magnifying Genomes)
First you need to create an agp file with the perl script fa2agp2.pl (https://www.hmpdacc.org/hmp/doc/fasta2apg.pl)

Then, you **annotate** your organism/bacterial **16s RNA sequences** through **RDP classifier** which is the **taxonomic identifier** linked with the **NCBI Taxonomy Browser**.

Finally, you need to fill the different field of the **submission** with the information you retrieved and upload the **agp and fasta files** you obtained with the execution of fa2agp.

# 3. Annotation with DFAST (a flexible prokaryotic genome annotation pipeline for faster genome publication)
You just need to put the assemblygenome.fasta file and give your email adress to receive the results.

# 4. Annotation with RAST (Rapid Annotation using Subsystem Technology)
You need to retrieve your **taxonomic identification** like with MaGe. 
Then, you give the proper file (assemblygenome.fasta) for submission.
After this step, you can choose between an old version and the recent one. In our study case, we used the recent one and it worked well.

# 5. Annotation with IMG (Integrated Microbial Genomes and Microbiomes)
To annotate with IMG you will need to create a new **Study in GOLD** (https://gold.jgi.doe.gov/project_submission) 
Then, **for each bacterial genome** you will be asked to create a **Sequencing Project** AND an **Analysis Project**.
You can Email to coresponding people on the platform to provide you a ready excel sheet to be filled which makes your task easier.