Bioinformatics Recipe Cookbook
Kraken2 classification validator

This recipe evaluates the accuracy of the Kraken 2 classification for selected markers.

1 result • updated 21 days ago by Istvan Albert

This recipe evaluates the accuracy of the Kraken 2 classification for selected markers.

The recipe generates simulated sequencing reads from NCBI accession numbers then performs classification with Kraken2.

In the third step evaluates and reports the accuracy (the percent of reads were classified correctly) of the classification.

The input to the recipe is a list of NCBI accession numbers:

AP012081
AP011279
DQ288268
AP014537

The main output is a file that lists the classification accuracy for each accession number:

accession     expect    actual   percent   taxid      title
AP012081      1000      993      99.3      67547      Margariscus margarita mitochondrial DNA, almost complete genome, except for D-loop
AP011279      1000      996      99.6      90988      Pimephales promelas mitochondrial DNA, complete genome
DQ288268      1000      996      99.6      8022       Oncorhynchus mykiss mitochondrion, complete genome
AP014537      1000      1000    100.0      27706      Micropterus salmoides mitochondrial DNA, almost complete genome
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