Mycobacterium whole genome sequencing

Question

[drparomita.bhatt]

Dear All, I am new to this community and hoping that it will help me regarding my scientific question. I'm doing research on Mycobacterium to answer the drug resistant patterns analysing the whole genome and I'm new to this field. May anyone kindly help me by suggesting that which sequencing platform will be better and what should be the sequence depth? I will grateful to you.

Answer 1

[lakhujanivijay]

It really depends on your research goals, the nature of your genome and the technology of sequencing.

If you have a reference genome and you are resequencing 15-20x coverage will be good enough to have an idea of the variation of your sample. However, if you are assembling it (de novo), then between 50 and 100x will be more than enough on Illumina platform.

Considering small size genome, you can go for pacbio sequencing or a with a hybrid approach i.e Illumina paired end 1X150 bp (short read) + pacbio, sequel / RS II platform (long read). Pacbio suggest 50X coverage. Also, suggesting to go through this paper

Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data

[drparomita.bhatt]

Thanks a lot Sir for your valuable suggestions.

[lakhujanivijay]

Dear Dr. Bhatt

Don't forget to follow up on your threads if something really helped.

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