[Question] Option to filter host's DNA

[matrs]

Hello,
I was wondering if you haven't tried to check for host DNA in the input files. I've seen some reports showing that it can be problematic for downstream analysis. I'm new analyzing metagenomes, so I'm not sure about it and maybe for your particular analysis this isn't a concern. Searching for software to do this, I found kneaddata, which separates bacterial DNA from host DNA, although it seems to include trimming too, which maybe isn't the most convenient.

https://huttenhower.sph.harvard.edu/kneaddata/

Jose Luis

[franciscozorrilla]

Hi Jose,

Thank you for your suggestions, KneadData or something similar may be a good addition for user cases where removing contaminants is imperative for analysis. Btw, if you want to filter out eukaryotic DNA you can also run EukRep on your assebmlies as shown here or see #14 . Having said that, KneadData would still be useful for removing eukaryotic reads from humans or other species.

Francisco

[matrs]

I see, that information about euKRep it's useful, I'll check it.

Thanks!