ANNOgesic 0.4.9

A bacterial transcriptome annotation pipeline based on RNA-Seq

About ANNOgesic

ANNOgesic is a modular, command-line tool that can integrated 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 gene, CDS/tRNA/rRNA, TSS and processing sites, transcripts, terminator, Untranslated region (UTR) as well as small RNA (sRNA), small open reading frame (sORF), circular RNA, CRISPR related RNAs, riboswitch and RNA-thermometer. It can also perform RNA-RNA and protein-protein interaction predictions. Furthermore, it groups genes into operon 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,tsspredator,optimize_tsspredator,terminator,transcript_assembly,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,tsspredator,optimize_tsspredator,terminator,transcript_assembly,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
                        Run RATT to transfer the annotation files from
                        reference to target.
    tsspredator         Run TSSpredator to predict TSSs or processing sites.
    optimize_tsspredator
                        Optimize TSSpredator based on (partial)manual detect
                        one.
    terminator          Detect rho-independant terminators.
    transcript_assembly
                        Run transcriptome assembly for detecting transcripts.
    utr                 Run UTR detection to detect 5'UTR and 3'UTR.
    srna                Detect intergenic, antisense and UTR-derived sRNA.
    sorf                Detect expressed sORF.
    promoter            Run MEME to dicover promoter.
    operon              Detect operon and sub-operon.
    circrna             Detect circular RNA by segemehl.
    go_term             Extract Go terms from Uniprot.
    srna_target         Detect sRNA-mRNA interaction by RNAup and RNAplex.
    snp                 Detect SNP/mutation and generate potential fasta file.
    ppi_network         Generate protein-protein interaction with literature
                        supported.
    subcellular_localization
                        Predict subcellular localization of genome CDS.
    riboswitch_thermometer
                        Predict riboswitch and RNA thermometer.
    crispr              Run CRT to predict CRISPR.
    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

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

Contact

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