Dear All,
I want to assembled mitochondrial genome from Illumina data of 150 bp Paired end libraries. I have got two file of 5 GB each in which about 29 millions read are present. When I have done Bowtie alignment with the closed relative, only about 60,000 read aligned into reference genome.
When I have combined these raw read for just to got a draft sequence, I got a file with about 2,98,000 bp in which 45 gene were predicted.
Now, Is it possible to get the whole mitochondrial genome from this data?
I think 10Gb data is quite much for assembling a complete mitochondrial genome because genes on mitochondrial genomes are preferred due to high copy number per cell, making them more likely be picked up than single-copy nuclear genes. You can test de novo assembly approach, just following this blog (https://comery.github.io/2018/11/07/Mitochondrioal-genome-assembly-appraches/) (and I suggest you pick ca. 3Gb data to have a try, 10Gb requires much computer memory and CPU), and wish this paper (Article Multiplex sequencing of pooled mitochondrial genomes - A cru...
) may help you.Good luck to you!
Dear Yang, Thanks for your suggestions. I have access to a server with up to 150 GB RAM. So, I will try to proceed complete data.
You might want to try MIRA, which works well for small genome de novo assembly like the mito genome. It worked in my hands earlier. I tried two versions v4.0 and v3.4, and for some reason v3.4 worked better. In my case it's for human mtDNA so I have a reference assembly to compare to. For my effort I used all reads (no duplicate reads removed), the assembly is close to the reference sequence. Hope this helps!
MitoZ: A toolkit for mitochondrial genome assembly, annotation and visualization(https://www.biorxiv.org/content/early/2018/12/07/489955) just preprinted on biorxiv.
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