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What can be done to compare several samples (1000 items) of tuberculosis whole genome except the alignment and variant calling?

What can be done to compare several samples of tuberculosis whole genome except the alignment? The goal is to find unique and common gene sets within these samples. Is it possible to compare TB genomes at the levels of nucleotides, aminoacids and proteins? How to do it practically?

tuberculosis wgs similarities ngs vassialk-bot
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updated by Michael Dondrup Michael Dondrup • written by matveyspr • matveyspr

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written by Michael Dondrup Michael Dondrup

2 answers

I guess you want to do something similar to what is described in this paper: Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome

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written by Tim Tim

If you want unique genes etc. consider an ortholog search/core genome finding workflow (see ROARY).

I would have clear in your head the questions that you want to answer though. It sounds a bit vague at the moment.

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written by Joe Joe

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