Determine my species from Isolates assemblies

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2.5 years ago

davidmaimoun ▴ 50

Hello,

If I have a genome assemblies from isolates, and I want to know what it is. More accurately, I need to know the isolates are Neisseria or H.Influenza, or not. I would like to query them against Refseq database to see if there are matches. Blast doesn't works good if I query a whole genome right? What is the better way to do that?

Thank you!

blast • 1.1k views

ADD COMMENT • link updated 2.1 years ago by Ram 44k • written 2.5 years ago by davidmaimoun ▴ 50

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As a first approach try TYGS

ADD REPLY • link 2.5 years ago by andres.firrincieli 3.8k

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Thank you Andres

I tried it but it is very slow

ADD REPLY • link 2.5 years ago by davidmaimoun ▴ 50

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Hi David,

how many genomes do you have?

ADD REPLY • link 2.5 years ago by andres.firrincieli 3.8k

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I have 8, We need to use tool that give an answer rapidly to know what to do with the patients The TYGS gave me a pretty good answer though, thank you for the tip. It take time but identified the right specie

ADD REPLY • link 2.5 years ago by davidmaimoun ▴ 50

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May I ask why you are running assemblies first, if speed is paramount? You could e.g. run StrainPhlAn3 directly on the raw reads...you would need to run it with the --add_viruses parameter to include Influenza, though.

If all that interests you, is if Neisseria and/or Influenza or neither is contained in an isolate, you can certainly speed up your analysis by building a custom reference set with just those and a few controls and then use a kmer-based alignment-free classification.