# Panaroo ## Installation Although Panaroo supports the latest version of python, currently Bioconda does not support versions >= 3.10 for all packages. An older version of python can be installed by creating an environment as ``` conda create -n panaroo python=3.9 conda activate panaroo ``` Panaroo can then be installed by running the following within a conda environment `conda install -c conda-forge -c bioconda -c defaults 'panaroo>=1.3'` ## Analysis ### Input format Panaroo now supports multiple input formats. To use non-standard **GFF3** files you must profile the input file as a list in a text file (one per line). Separate **GFF** and **FASTA** files can be provided per isolate by providing each file delimited by a space or a tab. Genbank file formats are also supported with extensions `'.gbk', '.gb' or '.gbff'`. These must compliant with Genbank/ENA/DDJB. This can be forced in Prokka by specifying the `--compliance` parameter. **NOTE:** Some annotations file such as those from RefSeq include annotations that break some of the assumptions of Panaroo. These include gene annotations of unusual length or that with premature stop codons (pseudogenes). By default Panaroo will throw an error if it encounters these annotations. You can automatically filter out such annotations by calling panaroo with the `--remove-invalid-genes` flag. ### Clean mode: strict By default Panaroo runs in its strictest (most conservative) mode. We have found that for most use cases this removes potential sources of contamination and error whilst retaining the majority of genes researchers are interested in. `panaroo -i *.gff -o results --clean-mode strict` ### Clean mode: sensitive Very rare plasmids are difficult to distinguish from contamination. Thus, if you are interested in retaining such plasmids at the expense of added contamination we recommend running panaroo using its most sensitive mode. `panaroo -i *.gff -o results --clean-mode sensitive` ### Para grafica utilizar gephi y verificar el proceso en la pagina de panaroo ### Exportar grafico para publicacion interactivo https://blog.miz.space/tutorial/2020/01/05/gephi-tutorial-sigma-js-plugin-publishing-interactive-graph-online/ python -m SimpleHTTPServer http://localhost:8000/ y luego abrir la carpeta que se descargo como exportada de sigma js