Hi, everyone.
I have some mitochondrial DNA data that was obtained using NGS technology. What I would like to know is which software program I can use to analyse my data.
I am currently undertaking a population genetic study on cichlids.
Looking forward to hearing from any of you.
Regards,
Darlington
Hi,
You might think to purchase a good software to assemble and analyse your data. I would recommend Geneious Prime. Other option is Sequencher. Some free tools are available but you would face of some difficulties i.e. you need different tools for each step.
Sincerely
The only single software for NGS analysis is CLC Genomics which I recommend to buy it!
In Geneious, you can assemble your reads on a template mitochondrial sequence. You can obtain it from genbank by finding the organism most closely related to the one you're studying.
Let's assume you want to assemble the complete mtDNA from a cichlid, then you go to the taxonomy browser in GenBank and enter Cichlidae in the search field, then click on the nameCichlidae at the top of the list. That will take you to a page where you see a box with the heading "Entrez records". In that box there is a line "Nucleotide". Click on the number (almost four million sequences) in that line, in the column "Subtree links". On the next page you get to, there is a search line, where you type "mitochondrion". Clicking Search will take you to a page that displays a number of complete mitochondrial sequences (16632bp, 16467 bp). Click on "FASTA" for one of them that is as closely related to your fish as possible and download. If you use this fasta sequence as template, your NGS reads may be assembled to the complete mitochondrion of your cichlid in Geneious. When that is done, you can find and extract sequences of various genes from your own sequence, e.g. d-loop, cytochrome b, ND2, CO1, 12s, 16s, if you don't want to compare the whole sequence to other samples you have. If you want to build a tree, you can use the free BEAST package, if you want to study population genetics, you can use the free DNAsp, as well as various R packages.
For annotation you may use Geneious, as proposed by others. In some cases, MITOS can also do a decent job http://mitos2.bioinf.uni-leipzig.de/index.py, but in both cases you have to check the results manually.
For comparative mitogenomic and phylogenetic analyses, you may try PhyloSuite, as it was designed to handle mitogenomic data: https://dongzhang0725.github.io/