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:


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

Calculate time to estimate copy number using your own parameters: fastMitoCalc vs. mitoCalc

# of samples (e.g. 10000):
Average coverage (e.g. 4 for 4x coverage, number only):
# of CPUs (e.g. 100):


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



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