A typical workflow in a genomics project would be to compare your newly sequenced/assembled/annotated genome to other organisms. The impetus behind
funannotate compare was that there was previously no way to easily compare multiple genomes. Funannotate stores all annotation in GenBank flat file format, while some people don’t like this format as it is difficult to parse with standard unix tools, the main advantage is that the annotation can be stored in a standardized format and retrieved in the same way for each genome. GFF3 is the common output of many annotation tools, however, this doesn’t work well for functional annotation as all of the “information” is stored in a single column. At any rate,
funannotate compare can take either folders containing “funannotated” genomes or GBK files –> the output is stats, graphs, CSV files, phylogeny, etc all summarized in HTML format.
Usage: funannotate compare <arguments> version: 1.8.14 Description: Script does light-weight comparative genomics between funannotated genomes. Output is graphs, phylogeny, CSV files, etc --> visualized in web-browser. Required: -i, --input List of funannotate genome folders or GBK files Optional: -o, --out Output folder name. Default: funannotate_compare -d, --database Path to funannotate database. Default: $FUNANNOTATE_DB --cpus Number of CPUs to use. Default: 2 --run_dnds Calculate dN/dS ratio on all orthologs. [estimate,full] --go_fdr P-value for FDR GO-enrichment. Default: 0.05 --heatmap_stdev Cut-off for heatmap. Default: 1.0 --num_orthos Number of Single-copy orthologs to use for ML. Default: 500 --bootstrap Number of boostrap replicates to run with RAxML. Default: 100 --outgroup Name of species to use for ML outgroup. Default: no outgroup --proteinortho ProteinOrtho5 POFF results. --ml_method Maxmimum Likelihood method: Default: raxml [raxml,iqtree] --ml_model Substitution model for IQtree. Default: modelfinder --no-progress Do not print progress to stdout for long sub jobs