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Filter human parasites from taxonomic profiling with Kraken
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20 months ago
Fungsten • 0

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:

https://ccb.jhu.edu/data/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?

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14 months ago
Asaf 5.6k
Israel

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.

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13 months ago
ctseto • 70

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.

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