We used MitoFinder to identify and annotate mtDNA.
git repo: https://github.com/RemiAllio/MitoFinder
MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics Mol Ecol Resour. 2020 Jul; 20(4): 892–905. Published online 2020 Apr 25. doi: 10.1111/1755-0998.13160
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This step should be performed after the scaffolding steps described in this repo
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singularity
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MitoFinder v 1.4
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reference mitochondrial genome in GenBank format https://www.ncbi.nlm.nih.gov/genome/browse#!/organelles/
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slurm workload manager https://slurm.schedmd.com/documentation.html
MitoFinder needs not only the target genome file, but also the reference mitochondrial genome of a close species. This file should be in GenBank format. This step cannot be automated. We only provide the NCBI download page for all mitochondrial genomes they have.
MitFinder is a container that can be run with singularity.
Edit the script with your information before launching it.
MitoFinder writes a log file with a summary of the analysis.
Example:
... MitoFinder found a single mitochondrial contig Checking resulting contig for circularization... Evidences of circularization were found! Sequence is going to be trimmed according to circularization position. Creating summary statistics for the mtDNA contig Annotating tRNA annotation with MitFi run well. Annotation completed Creating GFF and fasta files. Note: 15 genes were found in mtDNA_contig
Example:
EB1_MitoFinder_whole_genome_final_genes_AA.fasta.gz EB1_MitoFinder_whole_genome_final_genes_NT.fasta.gz EB1_MitoFinder_whole_genome.infos EB1_MitoFinder_whole_genome_mtDNA_contig.fasta.gz EB1_MitoFinder_whole_genome_mtDNA_contig.gb EB1_MitoFinder_whole_genome_mtDNA_contig_genes_AA.fasta.gz EB1_MitoFinder_whole_genome_mtDNA_contig_genes_NT.fasta.gz EB1_MitoFinder_whole_genome_mtDNA_contig.gff EB1_MitoFinder_whole_genome_mtDNA_contig.tbl
The BOLD Identification System (IDS) for COI accepts sequences from the 5' region of the mitochondrial Cytochrome c oxidase subunit I gene and returns a species-level identification when one is possible. Further validation with independent genetic markers will be desirable in some forensic applications.
https://www.boldsystems.org/index.php/IDS_OpenIdEngine
Include here how the COI fasta sequence is recovered from the MitoFinder results
Load the file to http://wolfe.ucd.ie/GenomeVx/
Include here which file is loaded to this web server