The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Mikado is a lightweight Python3 pipeline to identify the most useful or “best” set of transcripts from multiple transcript assemblies. See the above link for the complete documentation.

Quick Start

You can run three versions of Mikado: Mikado (will perform the whole workflow), Mikado util and Mikado compare. These have the same meaning as the commands you may run from command line and you can look up in the docs for further explenations.

Test Data

Test data can be downloaded from the GitHub repository.

Input File(s)

Inputs file will depend on the mode you are running Mikado:

  • Mikado:
    • genome FASTA file*
    • input GFF/GTF file(s)*
    • mutation file
    • scoring yaml file
    • bed file with splicing junctions
    • blast database for deriving homology informations
    • ORF BED file(s)*
  • MikadoCompare:
    • genome FASTA file*
    • prediction annotation file
  • MikadoUtil:
    • gtf file
    • id file
    • gff file
    • xml
    • reference GFF/GTF output file
    For this last step is advisable to look more extensively in the docs, as there are many sub-modes available.

Output Files

  • #.err, #.log, #.out - standard error, out and log
  • multiple files depending on the mode and arguments given may be returned

Tool Source for App


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