Question: Filter human parasites from taxonomic profiling with Kraken
gravatar for Fungsten
9 months ago by
Fungsten0 wrote:

I am trying to generate a summary of parasites in human metagenomic samples.

I have been looking into Kraken2 and its databases built from Refseq (which should contain all parasite sequences annotated). Have also noticed this DB available from EuPathDB:

Is it a good approach to solely use EupathDB or should I be looking into other DBs for any missing parasites that might not be included there?

ADD COMMENTlink modified 8 months ago by ctseto250 • written 9 months ago by Fungsten0
gravatar for Asaf
9 months ago by
Asaf6.5k wrote:

I personally think that if you're looking into parasites specifically your better option is to have a protein dataset and diamond blastx your DNA against it. I think that it will yield better results than using k-mer based methods.

ADD COMMENTlink written 9 months ago by Asaf6.5k

Could you explain why? Do parasites tend to have higher mutation rates?

ADD REPLYlink written 10 weeks ago by BioinformaticsLad140

Me today is trying to understand what me six months ago meant. I think that it's true for everything, not just parasites.

ADD REPLYlink written 10 weeks ago by Asaf6.5k
gravatar for ctseto
8 months ago by
ctseto250 wrote:

Using CAT (which in turn uses diamond), and then parsing its contig2classification output files by taxonomy may be helpful; everything with a taxonomy tree that descends towards parasites could then be eliminated.

ADD COMMENTlink written 8 months ago by ctseto250
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