Workflow for Metagenome annotation

This workflow is based on the JGI/IMG annotation pipeline (details). This is still in progress. It takes assembled metagenomes and generates structrual and functional annotations.

Running Workflow in Cromwell

This pipeline is being tested. Instructions will be posted in the future.

The Docker image can be found here

microbiomedata/mg-annotation

Input files

expects: fasta

Output files

Multiple GFF files.  More details to come.

Environment

• Linux (with sh/bash)
• Python >= 3.6 (via conda)
• Java >= 1.8 (via conda)

Third party software used (+ their licenses)

• Conda (3-clause BSD)
• tRNAscan-SE >= 2.0 (GNU GPL v3)
• Infernal 1.1.2 (BSD)
• CRT-CLI 1.8 (Public domain software, last official version is 1.2, I made changes to it based on Natalia's and David's suggestions)
• Prodigal 2.6.3 (GNU GPL v3)
• GeneMarkS-2 >= 1.07 (Academic license for GeneMark family software)
• Last >= 983 (GNU GPL v3)
• HMMER 3.1b2 (3-clause BSD, I am using Bill's thread optimized hmmsearch)
• SignalP 4.1 (Academic)
• TMHMM 2.0 (Academic)

Databases used (+ their licenses):

• Rfam (public domain/CC0 1.0; more info
• KEGG (paid subscription, getting KOs/ECs indirectly via IMG NR; more info
• SMART (restrictive license/custom); more info
• COG (copyright/unlicensed); more info
• TIGRFAM (copyleft/LGPL 2.0 or later); more info
• SUPERFAMILY (permissive/custom); more info
• Pfam (public domain/ CC0 1.0); more info
• Cath-FunFam (permissive/CC BY 4.0); more info