Displaying 1 to 6 from 6 results

ncbitax2lin - Convert NCBI taxonomy dump into lineages

  •    Python

All pre-converted lineages are hosted on ncbitax2lin-lineages, a GitLab repo, which allows pushing larger files without Git LFS and a bigger repo size limit. Regeneration is straightforward, but it may incur quite a bit of memory (~20 GB). I generated lineages.csv.gz on a machine with 32 GB memory. Pull request on refactoring to a lower memory usage is welcome. It's mainly about this line, where the pool.map takes places.

icn3d - WebGL-based 3D structure viewer

  •    Javascript

We provided two types of iCn3D widgets: basic interface and advanced interface. Either of these widgets could be easily added to your own web pages. Please see the help page for more details.

taxadb - :hatching_chick: locally query the ncbi taxonomy

  •    Python

Taxadb is an application to locally query the ncbi taxonomy. Taxadb is written in python, and access its database using the peewee library. Get the taxid from a scientific name.




ncbi-genome-download - Scripts to download genomes from the NCBI FTP servers

  •    Python

Some script to download bacterial and fungal genomes from NCBI after they restructured their FTP a while ago. Idea shamelessly stolen from Mick Watson's Kraken downloader scripts that can also be found in Mick's GitHub repo. However, Mick's scripts are written in Perl specific to actually building a Kraken database (as advertised).

bionode-ncbi - Node.js module for working with the NCBI API (aka e-utils).

  •    Javascript

To use bionode-ncbi as a command line tool, you can install it globally with -g. Or, if you want to use it as a JavaScript library, you need to install it in your local project folder inside the node_modules directory by doing the same command without -g.