- Dataset S3: in folder ./data
- Stable release: V0.99 [link]
The easiest way to install all dependencies is conda throught bioconda.
conda install -c bioconda \
biopython pysam seqtk bwa infernal=1.0.2 spades
git clone https://github.com/Runsheng/mitovar.git
export PATH="mitovar_install_path":$PATH
- fastq-dump (from sra-toolkit): if start from sra file other than fastq
- The pre-compiled exonerate only works on Linux x64 system, tested in Ubuntu 16.04, 14.04 and CentOS 7.
- anno: annotate a mtDNA fasta sequences and generate a tbl file for genbank submission
- assemble: assemble the mtDNA fasta file from a NGS fastq file and a nearby reference file
An example to run annotation command:
mitovar.py anno -f mtDNA.fasta -c protein.fasta -r rrna.fasta -s name
Or you can use the test file inside the test folder to make a testrun:
mitovar.py anno -f 1561998.fasta -c celmt_p.fasta -r rrna.fasta -s ctro
An example to run assemble command:
Note: put all fastq files in ./{spe}/fastq, and run command in ./
For instance, the species name {spe} is cbr
run the following command in /home/user, the fastq should be in /home/usr/cbr/fastq
mitovar.py assemble -f cel.fa -p 32 -s cbr