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MagicLamp - YfGenie

A software package for annotation of genomic datasets using discreet HMM sets.

pipeline

Citing MagicLamp

There is no official publication for MagicLamp. If it was useful for your work, please cite as follows:

Garber, AI., Ramirez, GA., Merino, N., Pavia MJ., McAllister, SM. (2020) MagicLamp: toolkit for annotation of genomic data using discreet and curated HMM sets. 2023: MagicLamp, GitHub repository: https://github.com/Arkadiy-Garber/MagicLamp.

Special thanks to AstrobioMike and his bit software package for enabling easy access to NCBI's RefSeq and GenBank assemblies.

Installation (Conda is required for this software)

git clone https://github.com/Arkadiy-Garber/MagicLamp.git
cd MagicLamp
conda create -n magiclamp -c bioconda -c conda-forge -c defaults -c astrobiomike hmmer bit --yes
conda activate magiclamp

Usage

Using your own HMM set with YfGenie

YfGenie.py --hmm -d HMMs_dir -a GCF_023585845.1 -o GCF_023585845.1 -t 16

- In the above command GCF_023585845.1 represents the RefSeq assembly accession.

- HMMs_dir is the folder containing raw HMM files. See the subfolders inside the hmms directory to see what these look like.

- You can also provide a meta-data file via the -m argument with gene and pathway names for each provided HMM (formatted after the hmm_summary.csv file in this repo).

Relying on annotation within GFF file (recommended if the gene/pathway is well-annotated)

YfGenie.py --gff -y genes.tsv -a GCF_023585845.1 -o GCF_023585845.1 -t 16

- genes.tsv is a single-column file listing gene names of interest (example file of the same names can be found in this repo).

Simply extracting amino acid usage frequencies and GC content from the provided genome assembly

YfGenie.py --gc -a GCF_023585845.1 -o GCF_023585845.1 -t 16

- this will generate a single-line TSV file that lists usage frequences for each amino acid residue.

The works (YfGenie can be run in multiple modes at once)

YfGenie.py --hmm --gff --gc -d HMMs_dir -y genes.tsv -a GCF_023585845.1 -o GCF_023585845.1 -t 16

You can also provide locally annotated files via the -c CONTIGS, -g GFF, and -p PROTs arguments

YfGenie.py --hmm --gff --gc -d HMMs_dir -y genes.tsv -c genome.fa -g genome.gff -p genome.faa -o genome_out -t 16

Example command providing multiple assemblies at a time:

while read i; do
    YfGenie.py -a $i -o $i -t 16 --hmm -d HMMs_dir --gc
done < genomes.txt

- the above command is a "while loop", where genomes.txt is a single-column text file that contains a list of RefSeq or GenBank assemblies (see example file in this repo)