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.
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" />
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
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
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