Tiara_mitogenomics
This is a snakemake workflow for detection, and preliminary annotation mitochondrial genomes of Metazoans (Animals) such as Nematodes in an assembled metagenomic data.
Note!
Before analysis you need to set up conda environment with snakemake installed.
Usage
git clone https://github.com/mkarlik93/tiara_mitogenomics
cd tiara_mitogenomics
conda activate snakemake
Input file, database and minimum length must be specified in config file as full paths - a template of config file you can find in config subfolder and looks like this:
run_name: test_run # Name of your run
assembly_path: "metagenomic_assembly.fasta" # A full path to metagenomic assembly
outputdir: 'test_run/' # An output directory
Pipeline_settings :
mito_pipline : True
General_parameters:
min_length: 3000 # A minimum length of contigs analyzed by tiara
temporary_directory: "~/." # Path to temporary directory
database: "Nematoda_CDS_protein.fa" # A full path to the database
When you modified config file (which must be located in config subfolder) you can start your analysis.
snakemake --use-conda --cores n , where n is the number of cores you want to be used. Remember you must be in tiara_mitogenomics folder.
MT_database can be downloaded from figshare contains representative proteomes specific for 12 group of Metazoa:
- Annelida-segmented-worms
- Arthropoda
- Bryozoa
- Chaetognatha
- Chordata
- Cnidaria
- Echinodermata
- Mollusca
- Nematoda
- Nemertea-ribbon-worms
- Platyhelminthes-flatworms
- Porifera-sponges
Please unzip datapack and specify path in config file
Also you can find concatenated proteomes from all groups in Animal_CDS_protein.fa
This database was created by developers of mitoZ please, credit their work as well.
Results
The main result is a tabular file with a suffix "_tabulated_result.tsv" that contains a names of contigs with counts of mitochondrial genes.
| Name | Length | GC_content | ND2 | ND5 | COX3 | ATP8 | ND6 | ND4L | ND4 | ND3 | ND1 | COX1 | ATP6 | CYTB | COX2 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Dummy_contig1 | 3072 | 23.14 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 7 | 0 | 1 | 0 |
Also you will find two subdirectories named "tiara_results" and "invidual_contigs_res". First contains native results of tiara analysis, the second one contains DNA and AA sequences originated from mitochondrial contigs with raw mmseqs2 reciprocal analysis.
Citation
Using this package please cite tiara