Arkadiy-Garber/FeGenie

HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes

FeGenie

Please see the Wiki page for introduction and tutorial on how to use this tool.

Citing FeGenie:

Garber AI, Nealson KH, Okamoto A, McAllister SM, Chan CS, Barco RA and Merino N (2020) FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies. Front. Microbiol. 11:37. doi: 10.3389/fmicb.2020.00037

Special thanks to Michael Lee for helping to put together the Conda environment for FeGenie. Thanks to Natasha Pavlovikj for creating the Conda recipe for FeGenie. Thanks to Michał Sitko for creating a Dockerfile for FeGenie.

Easy Installation (if you have Conda installed)

conda create -n fegenie -c conda-forge -c bioconda -c defaults fegenie=1.0 --yes
conda activate fegenie
FeGenie.py -h

and when you are done using FeGenie and would like to deactivate the Conda environment for FeGenie

conda deactivate

Installation (if you don't have Conda)

git clone https://github.com/Arkadiy-Garber/FeGenie.git
cd FeGenie
bash setup.sh
./FeGenie.py -h

Quick-start

FeGenie.py -bin_dir /directory/of/bins/ -bin_ext fasta -t 16

The argument for -bin_ext needs to represent the filename extension of the FASTA files in the selected directory that you would like analyzed (e.g. fa, fasta, fna, etc).

Quick-start (if you installed using the 'setup_noconda.sh' script)

./FeGenie.py -bin_dir /directory/of/bins/ -bin_ext fasta -t 16 -out output_fegenie

hmms/iron directory can be found within FeGenie's main repository -t 8 means that 8 threads will be used for HMMER and BLAST. If you have less than 16 available on your system, set this number lower (default = 1)

Tutorial (Binder)

FeGenie introductory slideshow:

Content | Video presentation

FeGenie video tutorial:

Content | Video presentation

To start the tutorial, hit the 'launch binder' button below, and follow the commands in 'Walkthrough'

(Initially forked from here. Thank you to the awesome binder team!)

Walkthrough

Enter the main FeGenie directory

cd FeGenie

print the FeGenie help menu

FeGenie -h

run FeGenie on test dataset

FeGenie.py -bin_dir genomes/ -bin_ext fna -out fegenie_out

Go into the output directory and check out the output files

cd fegenie_out
less FeGenie-geneSummary-clusters.csv

run FeGenie on gene calls

FeGenie.py -bin_dir ORFs/ -bin_ext faa -out fegenie_out --orfs

run FeGenie on gene calls, and use reference database (RefSeq sub-sample) for cross-validation

FeGenie.py -bin_dir ORFs/ -bin_ext faa -out fegenie_out --orfs -ref refseq_db/refseq_nr.sample.faa

Running with docker

In case of running FeGenie with docker the only dependency you need to have installed is docker itself (installation guide).

With docker installed you can run FeGenie in the following way:

docker run -it -v $(pwd):/data --env iron_hmms=/data/hmms/iron --env rscripts=/data/rscripts note/fegenie-deps ./FeGenie.py -bin_dir /data/test_dataset -bin_ext txt -out fegenie_out -t $(nproc)

./FeGenie.py ... follows normal, non-dockerized flow of arguments.

Beware that you need to mount directories which contain files FeGenie is supposed to read. If you are not familiar with docker then run docker run command from the directory into which you cloned FeGenie repository. If all the files you pass to FeGenie are in inside this directory and you use relative filepaths (like e.g. hmms/iron) everything will work just fine.

Upcoming Updates (we welcome more suggestions, which can be submitted as an Issue)

1. Ability to accept previously-annotated genomes and gene-calls.
2. Include Cytochrome 579 (and possible rusticyanin)
3. Improve dilineation between MtrA and MtoA for better resolution with respect to identification of iron reduction and iron oxidation, respectively.
4. Option to report absolute values for gene counts (rather than normalized gene counts)
5. Include option to release all results (regardless of whether rules for reporting were met)
6. Identification of iron-sulfur proteins.