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galaxy-tool-lca

A tool to determine the lowest common ancestor from BLAST results with taxonomy. This approach is partly based on MEGAN's (Huson et al., 2007) LCA method. This tool does not specifically use taxonids or separated mapping files. Instead, the script handles files with the taxonomy present in the last column of the input file. Those input files can be generated with our BLAST pipeline or you can create them manually.

Installation

Manual

Clone this repo in your Galaxy Tools directory:
git clone https://github.com/naturalis/galaxy-tool-lca

Make the scripts executable:
chmod 755 galaxy-tool-lca/lca.sh
chmod 755 galaxy-tool-lca/lca.py

Append the file tool_conf.xml:
<tool file="/path/to/Tools/galaxy-tool-lca/lca.xml" />

Ansible

Depending on your setup the ansible.builtin.git module could be used.
Install the tool by including the following in your dedicated *.yml file:

- repo: https://github.com/naturalis/galaxy-tool-lca
  file: lca.xml
  version: master

Information on tool usage, parameters and examples can be found here

How to cite

Beentjes KK, Speksnijder AGCL, Schilthuizen M, Hoogeveen M, Pastoor R, et al. (2019) Increased performance of DNA metabarcoding of macroinvertebrates by taxonomic sorting. PLOS ONE 14(12): e0226527. https://doi.org/10.1371/journal.pone.0226527

Source

Huson, D. H., Auch, A. F., Qi, J., & Schuster, S. C. (2007). MEGAN analysis of metagenomic data. Genome Research, 17(3), 377–386. http://doi.org/10.1101/gr.5969107