rRNA filtering for low RAM.

[raw937]

Hello,

I have these files with rRNAs. I have build my own custom silva database to eliminate them. However, the memory requirements appear to be quite high.

Also, I have noticed the rqcfilter.sh
I have found the riboKmers.fa.gz file testing bbduk. But, still the memory is quite high to use it.

What is your thought I the best way to filter rRNAs from metatranscriptomes with lowest memory and speed?

Is it better to use bbduk or rqcfilter?

Many thanks
Rick

[raw937]

I can use bowtie2 based. But, I am wanting to use bbduk or rqcfilter instead.