Ribosomal depletion percentage

Question

[Pin.Bioinf]

Hello, I want to observe the percentage of ribosomal depletion in my fastq files that were sequenced with NextSeq, how can I do that? I have never done this before. Is there a tool or script I can use?

Thank you

[Sej Modha]

You can try riboPicker.

The riboPicker tool can be used to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.

[h.mon]

In addition to riboPicker, you can also use SortMeRNA and BBDuk with the "ribokmers.fa" file. This later is my preferred approach, as it is really fast.