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Blast in metagenomics: should I download all NR database for this purpose?
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12 months ago
fhsantanna • 440
Brazil

Very basic question. I want to do a taxonomic analysis of an Iontorrent metagenomics data using MEGAN. I know that firstly I must blast the reads to a database (usually NR database from Genbank). I presume that this procedure should be done locally in order to process faster the data. So, I need to download all the NR database from Genbank. Is it correct?

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You can do nt or nr. Take a look at the MEGAN manual before you do blast. You would want to use standard text or XML format output for blast.

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OK. But it should be local, right? Blasting directly to the server is not appropriate, isn't it?

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If you don't have a lot of reads you can go with the server.

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What is a lot of reads? I have 500k reads.

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NCBI server won't accept 500K reads in one go. If you are able, do the search locally. That way you will have control over it.

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