ANNOgesic 0.5.6

A bacterial transcriptome annotation pipeline based on RNA-Seq

About ANNOgesic

ANNOgesic is a modular, command-line tool that can integrate different types of RNA-Seq data like dRNA-Seq or RNA-Seq generated after transcript fragmentation and generates high quality genome annotations. It can detect genes, CDSs/tRNAs/rRNAs, transcription starting sites (TSS) and processing sites, transcripts, terminators, untranslated regions (UTR) as well as small RNAs (sRNA), small open reading frames (sORF), circular RNAs, CRISPR related RNAs, riboswitches and RNA-thermometers. It can also perform RNA-RNA and protein-protein interactions prediction. Furthermore, it groups genes into operons and sub-operons and reveal promotor motifs. It can also allocate GO term and subcellular localization to genes. Several of ANNOgesic features are new implementation while others are performed and improved by third-party tools and for some of them adaptive parameter-optimizations were included. Additionally, numerous visualization and statistitcs help the user quickly evaluated feature predictions resulting from an ANNOgesic analysis. The pipeline is modular and was heavily tested with several RNA-Seq data set from bacterial as well as archaeal samples.

Documentation

Documentation can be found on here.

Installation

Short version (if you have all the requirements installed):

$ pip3 install ANNOgesic

If you want to know the requirement, please refer to Documentation.

Arguments

usage: annogesic [-h] [--version]
                 {create,get_input_files,get_target_fasta,annotation_transfer,tss_processing,optimize_tss_processing,terminator,transcript,utr,srna,sorf,promoter,operon,circrna,go_term,srna_target,snp,ppi_network,subcellular_localization,riboswitch_thermometer,crispr,merge_features,screenshot,color_png}
                 ...

positional arguments:
  {create,get_input_files,get_target_fasta,annotation_transfer,tss_processing,optimize_tss_processing,terminator,transcript,utr,srna,sorf,promoter,operon,circrna,go_term,srna_target,snp,ppi_network,subcellular_localization,riboswitch_thermometer,crispr,merge_features,screenshot,color_png}
                        commands
    create              Create a project
    get_input_files     Get required files. (i.e. annotation files, fasta
                        files)
    get_target_fasta    Get target fasta.
    annotation_transfer
                        Transfer the annotations from reference genome to
                        target genome.
    tss_processing      Detect TSSs or processing sites.
    optimize_tss_processing
                        Optimize TSSs or processing sites based on manual
                        detected ones.
    terminator          Detect rho-independant terminators.
    transcript          Detect transripts based on coverage file.
    utr                 Detect 5'UTRs and 3'UTRs.
    srna                Detect intergenic, antisense and UTR-derived sRNAs.
    sorf                Detect expressed sORFs.
    promoter            Discover promoter motifs.
    operon              Detect operons and sub-operons.
    circrna             Detect circular RNAs.
    go_term             Extract Go terms from Uniprot.
    srna_target         Detect sRNA-mRNA interactions.
    snp                 Detect SNP/mutation and generate potential fasta file.
    ppi_network         Detect protein-protein interactions with literature
                        supported.
    subcellular_localization
                        Predict subcellular localization of CDSs.
    riboswitch_thermometer
                        Predict riboswitches and RNA thermometers.
    crispr              Predict CRISPR related RNAs.
    merge_features      Merge all features to one gff file.
    screenshot          Generate screenshot for selected feature.
    color_png           Generate color screenshots of TSS or processing site.
                        It only works after running "screenshot" (after
                        running batch script).

optional arguments:
  -h, --help            show this help message and exit
  --version, -v         show version

License

ISCL (Internet Systems Consortium license ~ simplified BSD license) - see LICENSE

Contact

If you have any questions, please contact Sung-Huan Yu