Package: fcat
fCATOne of the critical steps in a genome sequencing project is to assess the completeness of the predicted gene set. The standard workflow starts with the identification of a set of core genes for the taxonomic group, in which the target species belongs to. The fraction of missing core genes serves then as a proxy of the target gene set completeness.fCAT is afeature-awareCompletenessAssessmentTool, that helps to answer the question "How complete is my gene set?". In particularly, fCAT checks for the presence of conserved genes (the core genes) of a specific taxonomy clade in the target gene set using feature-aware directed ortholog searchfDOG. In addition to the length criteria for classifying the found orthologs (as same asBUSCO), fCAT utilizes the domain architecture similarityFAS scoresto further validate the orthologs. The later gives an alternative view on the accuracy of the target gene models, which shows how different the target orthologs in comparison to the core genes in their domain architecture.fCAT outputs both the summary result in a tabular text file and the phylogenetic profile of the core genes, which can be visualized using the toolPhyloProfile. By analyzing the profiles of the entire orthologous groups within a specific taxonomy clade, we can further identify and ultimately correct erroneous gene annotations.Click here for the full PDF version of the ECCB2022 posterTable of ContentsHow to installUsageOutputfCAT score modesBugsContributorsHow-To CiteContactHow to installfCATtool is distributed as a python package calledfcat. It is compatible withPython ≥ v3.9.You can installfcatusingpip:python3 -m pip install fcator, in case you do not have admin rights, and don't use package systems likeAnacondato manage environments you need to use the--useroption:python3 -m pip install --user fcatand then add the following line to the end of your~/.bashrcor~/.bash_profilefile, restart the current terminal to apply the change (or typesource ~/.bashrc):export PATH=$HOME/.local/bin:$PATHNote:fCAT requiresRto be present! Please make sure that you have R installed on your computer.UsageThe complete process offCATcan be done using one functionfcatfcat --coreDir /path/to/fcat_data --coreSet eukaryota --refspecList "HOMSA@9606@2" --querySpecies /path/to/query.fa [--annoQuery /path/to/query.json] [--outDir /path/to/fcat/output]whereeukaryotais name of the fCAT core set (equivalent toBUSCOset);HOMSA@9606@2is the reference species from that core set that will be used for the ortholog search;queryis the name of species of interest. If--annoQuerynot specified,fCATfill do the feature annotation for the query proteins usingFAS tool.OutputYou will find the output in the/path/to/fcat/output/fcatOutput/eukaryota/query/folder, where/path/to/fcat/output/could be your current directory if you not specified--outDirwhen runningfcat. The following important output files/folders can be found:all_summary.txt: summary of the completeness assessment using all 4 score modesall_full.txt: the complete assessment of 4 score modes in tab delimited filefdogOutput.tar.gz: a zipped file of the ortholog search resultmode_1,mode_2,mode_3andmode_4: detailed output for each score modephyloprofileOutput: folder contains output phylogenetic profile data that can be used withPhyloProfile toolBesides, if you have already runfCATfor several query taxa with the same fCAT core set, you can find the merged phylogentic profiles for all of those taxa within the corresponding core set output (e.g./path/to/fcat/output/fcatOutput/eukaryota/*.phyloprofile).fCAT score modesThe table below explains how thespecific ortholog group cutoffsfor each fCAT core set were calculated, and whichvalue of the query orthologis used to assess its completeness, or more precisely, its functional equivalence to the ortholog group it belongs to. If the value of a query ortholog isnot less thanits ortholog group cutoff, that group will be evaluated assimilarorcomplete. In case co-orthologs have been predicted, the assessment for the core group will beduplicated. Depending on the value of each single ortholog, aduplicatedgroup can be seen asduplicated (similar)orduplicated (dissimilar)in the full report (e.g.all_full.txt).Score modeCutoffValue used for comparingMode 1 - Strict modeMean of FAS scores between all core orthologsMean of FAS scores between query ortholog and all core proteinsMode 2 - Reference modeMean of FAS scores between refspec and all other core orthologsMean of FAS scores between query ortholog and refspec proteinMode 3 - Relaxed modeThe lower bound of the confidence interval calculated by the distribution of all-vs-all FAS score in a core groupMean of FAS scores between query ortholog and all core proteinsMode 4 - Length modeMean and standard deviation of all core protein lengthsLength of query orthologNote:FAS scoresare bidirectional FAS scors;core proteinorcore orthologis protein in the core ortholog groups;query proteinorquery orthologis ortholog protein of query species;refspecis the specified reference speciesBugsAny bug reports or comments, suggestions are highly appreciated. Pleaseopen an issue on GitHubor be in touch via email.ContributorsVinh TranGiang NguyenIngo EbersbergerHow-To CiteTran V and Ebersberger I. fCAT: Assessing gene set completeness using domain-architecture aware targeted ortholog searches. F1000Research 2022, 11:1091 (poster) (doi:10.7490/f1000research.1119126.1)ContactFor further support or bug reports please contact:tran@bio.uni-frankfurt.de