Blast in metagenomics: should I download all NR database for this purpose?

Question

[fhsantanna]

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?

[GenoMax]

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.

[fhsantanna]

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

[Picasa]

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

[fhsantanna]

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

[GenoMax]

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.

Answer 1

[onestop_data]

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.

[cpad0112]

IMHO, Rapsearch is better than Diamond. Diamond is fast, but rapsearch is more sensitive, in my experience.

[onestop_data]

Sure. but will MEGAN take the Rapsearch2 output? I don't think so - that was the question on the post.

[cpad0112]

Yes. it does. Rapseach output is .m8 and .aln. @ metageni