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Tutorial: NCBI blast tutorial

I just posted a brief introduction to using NCBI blast tools from the command line, as well as how to speed up the blasts using gnu parallel, on GitHub.

The tutorial is available here: https://github.com/enormandeau/ncbi_blast_tutorial

I'm open to suggestions for improvements!

ncbi blast
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updated by Ram Ram • written by Eric Normandeau Eric Normandeau

1 answer

I think a small tutorial on how one can change the output format using -outfmt would be super beneficial. Just a few examples to show that you can fit the output for easier parsing etc...

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written by Jenez Jenez

I added a section with the different options for -outfmt.

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written by Eric Normandeau Eric Normandeau

I was hoping for it to be a bit more in-depth than what is posted currently. As a bare minimum I think at least one example of using say -outfmt '7 stitle sacc staxids pident evalue' should be in there, preferably showing how it affects the output. Having issues with a software, thinking you've found a tutorial with solutions only to find that it is lacking in details can be really frustrating. Do the noobs (including myself) a favour and post a bit of detail on the parts that are not super straight forward.

Then again, this might be outside of the scope of the tutorial as it only deals with ones own local database and not a full NCBI curated database.

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written by Jenez Jenez

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