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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fhsantanna
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I know this question is out, but I will make a comment which should help any person that looks for the topic here. I think the approach of running the alignment locally against the NR/NT database and inputting the alignments into MEGAN is fair.
The only important thing is that you should not use BLAST. This is going to be extremely slow. DIAMOND generates a similar output (if not the same) and should be 20x times faster than BLAST in some cases.
Sure. but will MEGAN take the Rapsearch2 output? I don't think so - that was the question on the post.
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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.
OK. But it should be local, right? Blasting directly to the server is not appropriate, isn't it?
If you don't have a lot of reads you can go with the server.
What is a lot of reads? I have 500k reads.
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.