Performance metrics of aligners and variant callers
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3 months ago
Prashant ▴ 10

I have microbial whole-genome sequence (WGS) data and I want to find SNPs and INDELs if present any. Before selecting a particular aligner or variant caller for this purpose, I want to check the performance metrics (accuracy, sensitivity, precision) of different aligners and variant callers using true variant data sets or simulated datasets. So, I have the following two questions:

  1. Is there any database from where I can get true variant data sets for microbial genome which I can use in assessing the performance metrics of different aligner or variant callers?

  2. Which is the best tool for generating simulated data set of microbial whole-genome sequence, that I can use in assessing the performance metrics?

Apart from this, if there is any other way for analyzing the performance metrics then please do tell.

Thank you in advance.

benchmarking WGS • 208 views
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Have you searched pubmed? By now there must be hundreds of papers that do this. Just read a few if you're uncertain which tools might work well.


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