EMMA: Metazoan Mitochondrial Annotator

(Currently EMMA is optimised for vertebrates, especially fish, but the intention is to make it broadly useful for most metazoan mitochondrial genomes)

Dependencies

EMMA relies on two amazing software packages from Sean Eddy's lab, HMMER and Infernal. Many programs from these packages must be accessible via your $PATH for Emma to function. Follow the installation instructions on the HMMER and Infernal websites to install these packages. EMMA is written in Julia; follow the download and installation instructions.

Installation

Clone this github repo:

git clone https://github.com/ian-small/Emma.git

Tell Julia to treat the repo as a Julia package:

julia

]

dev '~/github/Emma'

instantiate

(replace ~/github with whatever path you've cloned the Emma repo to)

This will install all the Julia packages that Emma needs, and the models it needs to annotate mitochondrial genomes.

You can now quit the Julia REPL with Ctrl-D

Running EMMA

julia --project=~/github/Emma ~/github/Emma/src/command.jl --help
Usage: Emma/src/command.jl [options]

Optional Arguments:

--invertebrates (flag) NCBI translation table for invertebrates instead of vertebrates (the default)

--rotate rotate genome and annotations to start with this feature

--fa file/dir for .fasta output

--gff file/dir for .gff output

--tbl file/dir for .tbl output (for GenBank submissions)

--svg file/dir for .svg output

Note: Use consistant inputs/outputs. If you wish to annotate a directory of fasta files, ensure that the output options are also directories.

Examples

To annotate a single genome in .gff format:

julia --project=~/github/Emma ~/github/Emma/src/command.jl --gff my_genome.gff my_genome.fasta

To rotate a single genome to start with MT-TM and save the rotated sequence in .fa format and the annotations in .gff format:

julia --project=~/github/Emma ~/github/Emma/src/command.jl --rotate MT-TM --fa my_genome.rotated.fasta --gff my_genome.rotated.gff my_genome.fasta

To annotate many fasta files in the directory 'my_genomes' and save the generated .tbl files in the same directory:

julia --project=~/github/Emma ~/github/Emma/src/command.jl --tbl my_genomes my_genomes

If you want some concurrency the add --threads=8 to the command line.

Install Emma as a package

You can also invoke Emma if you have it installed in your project (e.g. with say ] add https://github.com/ian-small/Emma.git).

julia --project=. -e 'using Emma; main()' -- --tbl my_genomes my_genomes

(Note the -- to separate julia options from Emma's.)