kb_gtdbtk

This is a KBase module generated by the KBase Software Development Kit (SDK).

You will need to have the SDK installed to use this module. Learn more about the SDK and how to use it.

You can also learn more about the apps implemented in this module from its catalog page or its spec file.

GTDB-Tk

This KBase apps wraps the GTDB-Tk commandline tool created by Donavan Parks, Pierre-Alain Chaumeil, and Phil Hugenholtz of the Austrailian Centre for Ecogenomics

GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).

References

A manuscript describing the GTDB-Tk is currently being prepared:

Chaumeil PA, Hugenholtz P, Parks DH. 2018. GTDB-Tk: A toolkit to classify genomes with the Genome Taxonomy Database. <in prep>.

In the meantime, if you find the GTDB-Tk useful please cite this GitHub page or the GTDB taxonomy:

Parks DH, et al. 2018. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol., http://dx.doi.org/10.1038/nbt.4229

We also strongly encourage you to cite the following 3rd party dependencies:

Matsen FA, Kodner RB, Armbrust EV. 2010. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics, 11:538.
Jain C, et al. 2017. High-throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries. bioRxiv, https://doi.org/10.1101/225342.
Hyatt D, et al. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11:119. doi: 10.1186/1471-2105-11-119.
Price MN, Dehal PS, Arkin AP. FastTree 2 - Approximately Maximum-Likelihood Trees for Large Alignments. PLoS One, 5, e9490.
Eddy SR. 2011. Accelerated profile HMM searches. PLOS Comp. Biol., 7:e1002195.

Setup and test

Add your KBase developer token to test_local/test.cfg and run the following:

$ make
$ kb-sdk test

After making any additional changes to this repo, run kb-sdk test again to verify that everything still works.

Installation from another module

To use this code in another SDK module, call kb-sdk install kb_gtdbtk in the other module's root directory.

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