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CrossClassify
CrossClassify is a tool for mapping results of metagenomic analyses from one taxonomy onto another. It is packaged with five taxonomies:
- SILVA 128 (29 Sep 2016)
- RDP release 11, update 5 (30 Sep 2016)
- Greengenes (May 2013)
- NCBI (5 Oct 2016)
- OTT version 2.10 draft 11 (10 Sep 2016)
Download
Click here to download CrossClassify.
Command line options
| Short | Full | Description | Default |
|---|---|---|---|
| -i | --in | input BIOM1 file. | |
| -r | --reference | reference taxonomy [ncbi/rdp/silva/gg/ott]. | ncbi |
| -o | --out | output BIOM1 file. | |
| -d | --dictionary | use synonim dictionary as provided by ncbi. | Off |
| -s | --strict | performs strict mapping (default mapping procedure is loose). | Off |
| -n | --nwk | print reference taxonomy as a newick file.Creates files <taxonomy>.tre and <taxonomy>.map for MEGAN. | Off |
| -hm | --heatmap | heatmap file. Saves summary of the cross mapping as a heatmap in a pdf file. | |
| -ps | --parallelsets | parallel sets file. Saves summary of the cross mapping as a parallel sets diagram in a pdf file. | |
| -v | --values | prints values of all parameters as set by the user or by default. | Off |
| -h | --help | prints this message. | Off |
Usage examples
We recommend allocating more heap space when running CrossClassify (e.g. with -Xmx6G, see here for more details).
Saving a whole taxonomy for viewing with MEGAN
java -Xmx6G -jar CrossClassify.jar -n -r rdp
Will produce rdp.tre, rdp.map and rdp.info files.
Mapping taxonomic assignments onto another taxonomy
java -Xmx6G -jar CrossClassify.jar -i <input>.biom -r silva -o <output_on_silva>.biom
Will map taxonomic paths in <input>.biom onto SILVA taxonomy and save results to <output_on_silva>.biom.
Use -s or --strict for strict mapping and -d or --dictionary if you want to use NCBI's synomin dictionary to correct for possible misspellings.
Mapping results are summarised as normalised dissimilarities and visualized as
- parallel sets (
-ps/--parallelsets <ps_file>.pdf) and - heatmaps (
-hm/--heatmap <hm_file>.pdf).
For more details please see paper.
Citing
If you use CrossClassify please cite:
Balvočiūtė M. & Huson D. H. SILVA, RDP, Greengenes, NCBI and OTT --- How do these taxonomies compare? 2016 Under Revision
Legal
CrossClassify is distributed under AGPL lisence
Taxonomic classifications in the data folder (packaged together with CrossClassify.jar) are under the following licences:
- SILVA SILVA Terms of Use/License Information
- RDP Creative Commons Attribution-ShareAlike 3.0 Unported License
- Greengenes Creative Commons Attribution-ShareAlike 3.0 Unported License
- NCBI
- OTT (see Scientific names of organisms: attribution, rights, and licensing)
Libraries
CrossClassify uses itext library for generating PDF files and json-simple for handling BIOM1 files.
Updated