About mit-o-matic

The diverse clinical spectrum of diseases manifested by mitochondrial dysfunction demands proper interpretation and analysis of mtDNA variants. mit-o-matic is a tool designed to provide clinically relevant information distributed in disparate resources for understanding and annotating mtDNA variations. The pipeline has two components: a command-line component that provides automation for alignment of NGS reads to the modified rCRS; and an online version that provides a comprehensive genetic report of mitochondrial variants, which includes information about the corresponding mutation, gene, associated phenotype and population frequency. It also reports the estimated haplogroup, disease associated variations and heteroplasmic sites.
Try out sample data  


Upload the fastq file (size < 25 MB)  

Read Length
Query Name
Alignment Tool
Heteroplasmy Frequency cut-off   %


Upload the parsed pileup file  

Paste the parsed pileup file  

Query Name
Heteroplasmy Frequency cut-off   %


Modified Reference Sequence - rCRSm 
For data with 51 bases of read length, 50 bases from the opposite end have been added at start and stop of rCRS

Download command-line version of mit-o-matic 

Citation: Velarikkal, S.K. and Dhiman, H. et. al. mit-o-matic: a comprehensive computational pipeline for clinical evaluation of mitochondrial variations from next-generation sequencing datasets. Hum Mutat. 2015 Feb 11. doi: 10.1002/humu.22767.
Funding and Support: This resource has been funded by Council of Scientific and Industrial Research (CSIR) - India, through Grant No. BSC0122 - CARDIOMED.
The resource is hosted by the Institute of Genomics and Integrative Biology (IGIB) - CSIR, and maintained by the Dr. Vinod Scaria Lab @ RNABiology.

* Paired end option has been deactivated temporarily because of some bugs in samtools. The updated version shall be available soon.