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Ribotricer Index Prepare Specifications

Process Details

  • Name: ribotricer_index_prepare
  • Process UUID: 0pl5t94sjh76xksuk7rc74v7319163
  • Process Group: ribosome_profiling

Overview

This process prepares Open Reading Frame (ORF) annotations for ribosome profiling analysis using ribotricer. It processes genome annotation files and reference sequences to generate ORF coordinate information required for downstream ribosome profiling analysis workflows.

This process is implemented in Bash, which invokes the ribotricer command-line tool for ORF preparation.

Key Functionality

  • ORF Annotation Preparation: Extracts and processes Open Reading Frame coordinates from GTF annotation files
  • Genome Integration: Combines genome sequence information with annotation data to create comprehensive ORF definitions
  • Index Generation: Produces formatted output files compatible with ribotricer's ribosome profiling analysis pipeline

Input/Output Specification

Inputs

Required Inputs

  • GTF File

    • Description: Gene annotation file containing transcript and exon coordinates
    • Format: GTF

  • Genome

    • Description: Reference genome sequence file
    • Format: FASTA

Outputs

  • Output File TSV
    • Description: Tab-separated values file containing prepared ORF annotations and coordinates for ribosome profiling analysis
    • Format: TSV

References & Resources

  • Tool Documentation: Contact the team for details on ribotricer usage and ORF preparation workflows
  • Related Papers: Choudhary, S., Li, W., & Smith, A. D. (2020). Accurate detection of short and long active ORFs using Ribo-seq data. Bioinformatics, 36(7), 2053-2059.