SPARCS is a snakemake pipeline for the transcriptome-wide prediction of riboSNitches.The SPARCS pipeline makes it easy to predict the effects of SNPs on RNA secondary structure.

Features

• Automatic dependency management

• Ability to utilize custom gene models

Documentation

• Installation
  • Prerequisites:
  • Installing the pipeline:
• Usage
• Input and Output Files
  • Input files
  • Output files:
• Config File

Guides

• Examples
  • Analyze a subset variants in the yeast genome
    • 1. Download the yeast genome and variants
    • 2. Run the SPARCS pipeline

If using SPARCS, please be sure to cite all relevant papers:

• Cingolani, Pablo. “Variant annotation and functional prediction: SnpEff.” Variant Calling: Methods and Protocols. New York, NY: Springer US, 2012. 289-314.

• Halvorsen, Matthew, et al. “Disease-associated mutations that alter the RNA structural ensemble.” PLoS genetics 6.8 (2010): e1001074.

• Lin, Jianan, et al. “Identification and analysis of RNA structural disruptions induced by single nucleotide variants using Riprap and RiboSNitchDB.” NAR Genomics and Bioinformatics 2.3 (2020): lqaa057.