runsheng / mitovar

Mitochondrial DNA sequence assembly and annotation for nematodes using NGS data.

Mitovar

Mitochondrial DNA sequence assembly and annotation for nematodes using NGS data.

• Dataset S3: in folder ./data
• Stable release: V0.99 [link]

Install

Install dependencies

The easiest way to install all dependencies is conda throught bioconda.

conda install -c bioconda \
    biopython pysam seqtk bwa infernal=1.0.2 spades 

Install mitovar (with mitfi and exonerate)

git clone https://github.com/Runsheng/mitovar.git

Add mitovar.py to $PATH

export PATH="mitovar_install_path":$PATH

Optional

• 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.

Run commands

The command contains:

• 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