ribodector to remove rRNA before classification

[LilyAnderssonLee]

Description of feature

ribodector: Accurate and rapid RiboRNA sequences Detector based on deep learning. To test whether Ribodector can effectively remove rRNA and improve classification performance.

[LilyAnderssonLee]

• Run ribodector after host-removal step
• Sample: One routine ticket in which rRNA was observed in Kraken2 classification results
• ribodector.sh:

  
  conda activate D_bioinfoTools_LAL

read1=$1 read2=$2 output1=$3 output2=$4

ribodetector_cpu -t 10 \ -l 151 \ -i $read1 $read2 \ -e rrna \ --chunk_size 256 \ -o $output1 $output2

Conclusion: The similar amount of rRNA was observed both with and without the Ribodector step. Therefore, Ribodector does not show significant performance improvement in this case. We could explore alternative tools for removing ribosomal RNA.

[sofstam]

Great that you tried this tool!