What stage of pre-processing in EBI data?

Question

[CAnna]

Hi,

I am trying to figure out the necessary pre-processing steps before using sequencing data retreived from online databases. I work with metagenomes from Huaman gut microbiome. I figured out that the main three steps for this type of data are:

1) Identify and mask Human reads

2) Remove duplicate reads

3) Trim low quality bases

Here is an example of a study from which I would like to use data.

I can't figure out at what stage those data are. I beleive Human reads masking should have been performed already, as this has to deal with subjects privacy/ethics. But I don't find a clear information telling me that this is the case or not. Are sequencing data available on inline repositories always already cleared of Human reads already?

Thank you, Camille

[GenoMax]

Assume that the provided data is raw, if there are no notes about it being processed. If all reads are the same length then it is not even scanned/trimmed.

I suggest that you use removehuman decontamination protocol using BBMap suite. Other tools in suite clumpify.sh (will help you remove dups) and bbduk.sh will help trim the data.

[CAnna]

Great, Thanks for the tools recommendation!