Question: Filter human parasites from taxonomic profiling with Kraken
0
gravatar for Fungsten
9 months ago by
Fungsten0
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:

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?

ADD COMMENTlink modified 8 months ago by ctseto250 • written 9 months ago by Fungsten0
1
gravatar for Asaf
9 months ago by
Asaf6.5k
Israel
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
1

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
0
gravatar for ctseto
8 months ago by
ctseto250
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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