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BioInfoTools / BBMap

(Not Offical) BBMap short read aligner, and other bioinformatic tools.
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rRNA filtering for low RAM. #24

Open raw937 opened 5 years ago

raw937 commented 5 years ago

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 commented 5 years ago

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