Dear all,
As far as we all know, doing blast in the NGS filed is really time-consuming and impossible in the routine way. Could anybody please let me know is there a free ultra-fast resource to be able to submit such a blast job there and get the output? Thanks in advance for your helpful comments.
3 answers
There are fast alternatives to blast, for example Diamond or RAPsearch2. Regarding seta's suggestion to use usearch. I participate in the development of a more sensitive version called vsearch (not faster than usearch though).
Hello,
You could have a look on the academic version of Klast; for instance, it provides the same quality as blast but is 5x faster than blastp and up to 10x faster than blastx.
If you have access to it, you can check this paper that compares some blast-like tools with the help on different quality metrics.
Thanks for your prompt feedback. I know it, but I don't work with it as I heard that it is not as sensitive as blast, it is? I would like to do "blastn" and "blastx" on assembled contigs of non-model plants, which has few sequencing data in the public resources, in your opinion, using of "usearch" instead of blast is a suitable in my case?
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Does your university or an associated group have a HPC cluster available? You could use this to parallelize your blast runs using tools like gnu parallel.