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Please help to choose Bioconductor R packages and other software for the whole genome sequence data analysis and, in particlular, the goals of false discovery mutation rate, mutations exclusion, mutation contribution and data dimensionality reduction. I could find Expander, MeV, Genesis software for the microarray experiments, however, could not find similar tools for the whole genome sequence analysis of mycobacteria. Sorry, that my question has no code.

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  • $\begingroup$ What is your question? $\endgroup$ – WYSIWYG Jan 10 '15 at 15:04
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    $\begingroup$ This is a good question! why is this getting close votes? it is slightly incoherent and badly written but it definitely merits a response! $\endgroup$ – Bez Jan 10 '15 at 16:06
  • $\begingroup$ Have you searched biostars.org? That is a bioinformatics board, and I'd say about half the content is about next gen sequencing. $\endgroup$ – swbarnes2 Jan 10 '15 at 17:57
  • $\begingroup$ @Bez I voted to close because I think (a) it is broad (b) I am not able to understand what is OP asking for exactly; some kind of all in one package? I retracted the vote but the question needs some clarification. $\endgroup$ – WYSIWYG Jan 11 '15 at 6:06
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There are couple of them. First if you want to sequence analysis basic packages are :

http://www.bioconductor.org/help/workflows/high-throughput-sequencing/

Also, Maqweb seems promising.

http://maqweb.sourceforge.net

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  • $\begingroup$ Add more software, including commercial, please, if you can $\endgroup$ – VassiaAlk Jan 11 '15 at 13:46

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