README.md

TERmitoGENOMES

Repository for mitogenome assembly and annotation in termites

Annotate mitogenomes

Dependencies: MitoFinder

## Get current database file to be used by MitoFinder's "--refseq"
wget https://raw.githubusercontent.com/sihellem/TERmitoGENOMES/master/reference_mitogenomes/v0/references.gb.gz && gzip -d references.gb.gz

### Annotation of mitochondrial scaffolds
MITO_REF=references.gb
ASSEMBLY=sample.fasta
ID=some_id

mitofinder \
  --processors ${SLURM_CPUS_PER_TASK} \
  --seqid $ID \
  --assembly $ASSEMBLY \
  --tRNA-annotation "mitfi" \
  --organism 5 \
  --refseq $MITO_REF

How to cite

Credits: Hellemans Simon.