Package: decouphage
Decouphage: the art of decorating a Phage genome by gluing feature cutouts into it.As the name suggests decouphage is a tool designed to annotate phage genomes. It only external dependency is ncbi-blast+
everything else is optional.Relevant branchesmain branch: stable version available inpypianddockerhub.dev branch: development branch with new features and bugs.Table of contentsHighlightsValidationHow can I use decouphageOptionsI want to discover and annotate a lot of ORFsI want to use prodigal to find my genesI have a genbank with poor annotation and want moreInstallationUbuntuDockerDatabasesDownloading databaseMaking custom databasesHighlightsCan be easily installed in Linux or Mac computers. Only requirement is ncbi-blast+.Can be extended with prodigal, but as default it uses phanotate for ORF calling.Decouphage is fast, using a Macbookmost phage genomes can be annotated in less than a minute.Uses ncbi NR database containing non-identical sequences from GenBank CDS translations, PDB, Swiss-Prot, PIR, and PRF.Allow manual curation using theweb interface.ValidationDecouphage validation was made in comparison to RAST(Rapid Annotation using Subsystem Technology), a tool that is often
praised for its good Prokaryotic annotation capabilities.Decouphage outperforms RAST when calling some of the most relevant product categories:The CDS annotation agreement between Decouphage and RAST is high, reaching up to 94% for some products:EnzymeAgreement rate with RASTendonuclease94%exonuclease58%helicase70%hydrolase73%kinase86%ligase94%methyltransferase65%polymerase76%primase78%protease85%recombinase28%reductase90%synthase84%terminase94%transferase60%A precise comparison of product-to-position is difficult given differences in spelling, typos, synonyms, and
interchangeable names, but the table above can give a good idea of the similarities.To corroborate the surplus of annotations that decouphage achieves, the amount of "hypothetical protein" and
"Phage protein" was also checked:ProductDecouphageRastAgreement rate with RASThypothetical protein3945630253%phage protein01626N/A1Total products96929692N/A2Decouphage does not include products containing "phage protein" as they usually are a noise source.The genbank file generated by RAST was used as input for decouphage to ensure no difference in the number of CDS.This table shows that Decouphage potentially assigns 2x more meaningful products than RAST when annotating a phage
genome.How can I use decouphageOptionsUsage: decouphage [OPTIONS] INPUT_FILE

Options:
  --prodigal             Use prodigal for orf calling instead of phanotate.
  -d, --db PATH
  -o, --output TEXT
  -t, --threads INTEGER  [default: 1]
  --tmpdir TEXT          Folder for intermediate files.
  --no_orf_calling       Annotate CDS from genbank file.
  --locus_tag TEXT       Locus tag prefix.
  --download_db          Download default database.
  -v, --verbose          More verbose logging for debugging purpose.
  --help                 Show this message and exit.I want to discover and annotate a lot of ORFsdecouphage genome.fasta -o genome.gbI want to use prodigal to find my genesdecouphage genome.fasta -o genome.gb --prodigalI have a genbank with poor annotation and want moreIn this mode decouphage will reuse the genbank ORFs and just run the annotation procedure.decouphage genome.gbk -o genome.gb --no-orf-callingInstallationYou have multiple options to install and run decouphage:UbuntuInstall decouphage:pip install decouphage(Required)Install ncbi-blast+apt install ncbi-blast+(Optional)Install dependencies:apt install prodigal trnascan-seDockerRun with docker (Already includes dependencies and databases):docker run decouphage/decouphageDatabasesDecouphage database is derived from NCBI NR database clustered at 90% identity and 90% sequence length.Downloading databaseDownload database to default location in $HOME/.decouphage/db/decouphage --download_dbMaking custom databasesMake blast databasemakeblastdb -in database.fa -parse_seqids -blastdb_version 5 -dbtype prot