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DaehwanKimLab / centrifuge

Classifier for metagenomic sequences
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kraken-style report #202

Closed chulghim closed 3 years ago

chulghim commented 3 years ago

1) Is the abundance value from kraken-style report normalized by its genomic length such as centrifuge-style report's seventh column?

2) Which of numReads and numUniqReads do you use to calculate abundances?

mourisl commented 3 years ago
  1. No, the abundance is not normalized by the genome length in report.
  2. I think it is the numReads, which should be the number of reads from the subtree in the taxonomy tree with the current taxonomy id as the root.