step by step BlastX against nr using Amazon cloud

Question

[Farbod]

Dear Biostars, Hi

I want to run blastx against NCBI nr for annotating thousands of de novo transcripts. I want to do it as fast as possible.

I have heard that one way is to use Amazon cloud. So, would you kindly help and introduce me any step-by-step manual or resource in this regard?

(e.g: where to begin? quantity of resources I need to rent from cloud and related costs? should I download the Nr database locally or downloading it into Amazon cloud? or uploading my transcriptome assembly into the Amazon? is there any pre-installed and ready to use Cloud for Bioinfirmatics (some BioCloud)? . . . and so on).

Thanks

Notes:

0- I have checked some Biostars posts but could not find any simple guidance.

1- I have no computational resources at home (no server and ...)

2- I do not want to use Blast2GO Pro CloudBlast (why? it is expensive for me!)

[Abhishek]

DIAMOND is basically meant for short reads for metagenome data. If you have longer sequences (say 1kb long), I don't think it will be the right choice.

Answer 1

[GenoMax]

Have you looked at the NCBI BLAST on Cloud help? There is step-by-step guidance available using links at the left.

That said, if you were looking to do this for thousands of transcripts then you should use DIAMOND instead. Regular blast+ may take too long and cost more.

There is also PAUDA.

[Farbod]

Thanks, Have you tried it? is it efficient (speed and cost)? I know that running local Diamond needs more than 32 GB of RAM. if it could be run on the cloud, it is a fast algorithm.

[GenoMax]

Be sure to test a small subset of data first to see what the costs would be. They would likely scale directly in relation to size of your query data and can add up.

[Farbod]

• I have found some youtube

[GenoMax]

Should be available here.

[Sej Modha]

I agree, DIAMOND is much faster than BLASTX, especially for large datasets.