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Check Build Salmon Index Specifications

Process Details

  • Name: Check Build Salmon Index
  • Process UUID: yRU8OHv92TqNeJoXj3ANsarQtY2zAF
  • Process Group: Index

Overview

This process builds a Salmon index for RNA-seq quantification if one does not already exist in the specified location. Salmon is a fast and accurate tool for transcript quantification from RNA-seq data that requires a pre-built index of the reference transcriptome. The process intelligently checks for an existing index and only builds a new one when necessary, saving computational time and resources.

This process is implemented in Bash, which invokes gffread and Salmon tools for transcriptome extraction and index construction.

Key Functionality

  • Index Validation: Checks if a Salmon index already exists at the specified location to avoid redundant computation
  • Transcriptome Extraction: Extracts transcript sequences from the reference genome using the provided GTF annotation file
  • Decoy-Aware Indexing: Creates a comprehensive index that includes both transcripts and genomic sequences as decoys to improve quantification accuracy
  • Conditional Execution: Only runs when Salmon quantification is enabled in the pipeline configuration

Input/Output Specification

Inputs

Required Inputs

  • genome

    • Description: Reference genome sequence file containing chromosomal DNA sequences
    • Format: FASTA

  • gtfFile

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

Outputs

  • salmon_index
    • Description: Complete Salmon index directory containing all necessary files for transcript quantification
    • Format: Folder

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Optional Salmon Index Parameters
    • Description: Optional salmon index parameters
    • Default value: (empty string)

References & Resources

  • Tool Documentation: Contact the team for details on Salmon indexing procedures
  • Related Papers: Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods, 14(4), 417-419. https://doi.org/10.1038/nmeth.4197