mitoAnalyzer
a software package for analyses of mitochondrial DNA using sequencing data
Overview
mitoAnalyzer is a software package that provides a general approach for the analysis of mitochondrial DNA (mtDNA) in next-generation sequencing studies, using whole-genome sequencing data. It has two components:
Genotype Likelihood Calculation
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Method for mitoCalc and fastMitoCalc
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Comparison of mitoCalc and fastMitoCalc
Program | Nuclear Genome Used as Reference | Total Length of Nuclear Genome Considered | Computing Time: 1 sample at 4x coverage, 1 CPU | Computing Time: 50,000 samples at 30x coverage, 500 CPUs |
---|---|---|---|---|
mitoCalc | Whole genome | 3.2 billion bases | 3 hours | 3 months |
fastMitoCalc | 3,000 1,000-bp fragments (default setting) | 3 million bases | 59 seconds | 12.5 hours |
fastMitoCalc is 180x faster than mitoCalc!
Calculate computing time for copy number estimation
mitoCalc time:
fastMitoCalc time:
Note: Calculation is a very rough estimate, actual calculation time will depend on situation-specific factors, such as i/o speed of cpu's. This calculation is optimistic, and therefore should serve only as a reference.
Assumptions: The formula used is: (# samples * coverage)/CPUs. This therefore assumes that an increase in either coverage or samples corresponds to a proportional increase in computation time, and that an increase in the number of CPUs corresponds to a proportional decrease in computation time. These assumptions are optimistic and will not hold for every case.
Calculator written by: TJ Butler
Current Directions
The software package was originally developed to analyze whole-genome sequencing data. We are actively investigating its applicability to exome-sequencing data.
Citation
Ding J*, Sidore C, Butler TJ, Wing MK, Qian Y, Meirelles O, Busonero F, Tsoi LC, Maschio A, Angius A, Kang HM, Nagaraja R, Cucca F, Abecasis GR, Schlessinger D* (2015). Assessing mitochondrial DNA variation and copy number in lymphocytes of ~2,000 Sardinians using tailored sequencing analysis tools. PLoS Genetics 11(7): e1005306. *corresponding author Link
Qian Y, Butler TJ, Opsahl-Ong K, Giroux N, Sidore C, Nagaraja R, Cucca F, Ferrucci L, Abecasis GR, Schlessinger D, Ding J*(2017). fastMitoCalc: an ultra-fast program to estimate mitochondrial DNA copy number from whole-genome sequences. Bioinformatics Pubmed . *corresponding author
Last update: Apr 14, 2017