This page assumes you already have some familiarity with working at the command line. NOTE: This stuff can look messy, mostly because it is it scares me too. This page holds some of the ways I’ve used EDirect, both to serve as a handy archive for myself, and to hopefully help others 🙂 It won’t be as comprehensive as most other things on this site, as it’s extremely expansive and it’s still nowhere near intuitive for me 🤷‍♂️ But these examples may do what is needed, and if not they at least might provide good starting points for building the code that will do what is needed. And I often end up digging through several of my old log files to find things, so…

But I still have trouble finding examples when I need them (and I always need them when using this). Those are where I’ve learned from (along with a lot of trial and error). There is a lot of info on this at the main NCBI EDirect page, and some more here. But like a lot of things, once I had a little familiarity with it, I started to appreciate how useful and powerful it can be.īeing able to access data and info from NCBI at the command line can allow us to: automate and document things well (we can give the exact command used to retrieve information and the date it was executed, rather than “pulled from NCBI”) download directly to a server rather than our local computer pull more specific information than we can on the site and more 🙂 Learning to use it at all was painful at times for me – and still is when I’m trying to figure out new stuff with it. EDirect is a set of tools NCBI provides to enable accessing the vast amount of information stored at NCBI from the command line.

I also put together a small program specifically for downloading assemblies by accession when making GToTree, and I found it useful in general so it’s also now part of my Bioinf Tools as bit-dl-ncbi-assemblies.īut there have been times when I needed more than these could offer, which required me spending a decent amount of time getting used to using NCBI’sĮDirect tools. For searching by taxonomy and downloading genomes (assemblies), and some others have put together a great tool called ncbi-genome-download, and they have one for downloading individual sequences by accession called ncbi-acc-download. There are some convenient tools available that may help in some situations depending on our needs. But sometimes it can be a little tricky to figure out how to download the data we want – particularly when it’s a lot of things and we want and/or need to do it at the command-line rather than at the site. Source-organism taxid and lineage from protein accession.Accessing taxonomy info from protein accessions.Protein annotations from assembly accession.

Change nuclotide contig in bioedit