Mt DNA haplogroup analysis from HTS data
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6.9 years ago
always_learning ★ 1.1k

Hello Every one !!

Happy New year to one and all!!

Could you please point me to some good tutorials/link/article/blog for Mt DNA haplogroup analysis ?

Thanks

Najeeb

Mt haplogroup • 1.8k views
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6.9 years ago
Vinod Scaria ▴ 10

Dear syednajeebashraf

You could find our resource mit-o-matic http://genome.igib.res.in/mitomatic/ which can handle NGS datasets for Haplogroup analysis

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6.9 years ago

If you attempt to haplotype your sequences through Mitomaster, please use the web service:
http://mitomaster.mitomap.org/cgi-bin/webservice.cgi

For a local run you might want to look at Phy-mer:
https://github.com/danielnavarrogomez/phy-mer

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6.9 years ago
rbagnall ★ 1.7k

I have sequenced the human Mt genome from off target exome sequencing reads using the method of:

Picardi E, Pesole G. Mitochondrial genomes gleaned from human whole-exome sequencing. Nat Methods. 2012;9(6):523-4.

 

I then used the resulting consensus Mt DNA sequence (in fasta format) to determine the haplogroup using a local installation of Mitotool:

http://www.mitotool.org/

 

 

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