Finding variations in mitochondrial genomes

Question

[ammarsabir15]

I am a beginner in ngs data analysis.I want to construct a linux based pipeline for finding variatioins in mitochondriala(mt) genomes (in fastq format) from revised cambridge reference sequence(in fasta format).? I there anyone to tell me how to construct this pipeline ??

Answer 1

[rbagnall]

A pipeline to sequence mitochondrial genome from off-target exome sequence data:

http://www.ncbi.nlm.nih.gov/pubmed/22669646

I found this to work well and the Python scripts are available from the Nature Methods website.

There is and another approach, called Mitoseek (not tested by me):

http://www.ncbi.nlm.nih.gov/pubmed/23471301

with scripts available at github:

https://github.com/riverlee/MitoSeek