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SpliceScape

With the increasing generation of RNAseq data, splicing analyses have become feasible. This process has revealed numerous functions attributed to splicing, including involvement in leaf morphogenesis, regulation of gene expression, and distinct splicing patterns between animals and plants. However, there are still few studies focused on generating splicing data to understand its applications.

SpliceScape is a bioinformatics pipeline designed for the large-scale identification and characterization of splicing events from RNA-Seq data. Built using the Nextflow workflow orchestrator, it provides an efficient, reproducible, and scalable solution for generating comprehensive splicing landscapes of an organism.

The pipeline automates all critical steps of splicing analysis, from raw data processing to the final characterization of events. It integrates state-of-the-art tools to ensure high accuracy and performance, including:

  • Data Cleaning: BBDuK
  • Splicing-Aware Alignment: STAR
  • Splicing Event Identification and Quantification: MAJIQ and SGSeq

This approach allows SpliceScape to handle large public datasets, making it a powerful tool for comparative transcriptomics and for exploring the dynamics of RNA processing.

📊 The diagram below provides an overview of the SpliceScape workflow, from the initial input files to the final results.

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✅ The pipeline is divided into distinct stages:

  1. Pre-processing: Metadata acquisition and filtering.
  2. Core Pipeline: Downloading reads, quality control (BBDuK), genome indexing (STAR), mapping (STAR), and splicing analysis (MAJIQ & SGSeq).
  3. Post-processing: Parsing and integrating results into a unified database.

Project overview

👆 Click on project steps bellow to see its details.

flowchart TD
    %% 1. Definição das Cores e Estilos
    classDef pre_processing fill:#D3D3D3,stroke:#36454F,stroke-width:2px,color:#36454F
    classDef input_files fill:#6b9d59,stroke:#36454F,stroke-width:2px,color:#36454F
    classDef main_header fill:#c179b0,stroke:#36454F,stroke-width:2px,color:#36454F,font-weight:bold
    classDef core_pipeline fill:#E0BBE4,stroke:#36454F,stroke-width:2px,color:#36454F
    classDef post_processing fill:#D3D3D3,stroke:#36454F,stroke-width:2px,color:#36454F
    classDef final_output fill:#00a1a9,stroke:#36454F,stroke-width:2px,color:#36454F

    %% 2. Definição dos Módulos com Links
    subgraph PRE-PROCESSING
        A("<a href='https://github.com/labbces/SpliceScape/wiki/0.1-Pre%E2%80%90processing:-SRR-metadata-DB-construction'>SRR metadata DB</a>")
        B("<a href='https://github.com/labbces/SpliceScape/wiki/0.2-Filter-SRRs'>Filter SRRs</a>")
    end
    
    C("<a href='https://github.com/labbces/SpliceScape/wiki/0.3-Input-Files:-Preparing-Genome-and-Transcriptome-Data'>Phytozome / Input files</a>")

    subgraph "PIPELINE"
        D("<a href='https://github.com/labbces/SpliceScape/wiki/1.0-SpliceScapeReads-Processing'>Reads processing</a>")
        E["<a href='https://github.com/labbces/SpliceScape/wiki/1.1-SpliceScape:-Downloading-Raw-Reads'>Downloading reads</a>"]
        F["<a href='https://github.com/labbces/SpliceScape/wiki/1.2-SpliceScape:-Read-Cleaning-with-BBDuK'>Cleaning - BBDuK</a>"]
        G["<a href='https://github.com/labbces/SpliceScape/wiki/1.3-SpliceScape:-Genome-Index-Generation-with-STAR'>Genome Generate - STAR</a>"]
        H["<a href='https://github.com/labbces/SpliceScape/wiki/1.4-SpliceScape:-Read-Mapping-with-STAR'>Mapping - STAR</a>"]
        I("<a href='https://github.com/labbces/SpliceScape/wiki/1.6-SpliceScape:-Splicing-Analysis-with-MAJIQ'>Splicing Analysis<br/>MAJIQ</a>")
        J("<a href='https://github.com/labbces/SpliceScape/wiki/1.5-SpliceScape:--Splicing-Analysis-with-SGSeq'>Splicing Analysis<br/>SGSeq</a>")
    end

    subgraph POST-PROCESSING
        K["<a href='https://github.com/labbces/SpliceScape/wiki/2.2-Post%E2%80%90Processing:-MAJIQ-Parser'>MAJIQ parser</a>"]
        L["<a href='https://github.com/labbces/SpliceScape/wiki/2.1-Post%E2%80%90Processing:-SGSeq-Parser'>SGSeq parser</a>"]
        M["<a href='https://github.com/labbces/SpliceScape/wiki/2.3-Post%E2%80%90Processing:-SGSeq-Parser'>Merging outputs</a>"]
    end

    N("<a href='https://github.com/labbces/SpliceScape/wiki/3.-Final-tables'>Final tables</a>")

    %% 3. Conexão dos Módulos
    A --> B
    C --> G
    B --> E
    E --> F
    F --> H
    G --> H
    H --> I & J
    I --> K
    J --> L
    K & L --> M
    M --> N
    
    %% 4. Aplicação dos Estilos
    class A,B pre_processing
    class C input_files
    class D main_header
    class E,F,G,H,I,J core_pipeline
    class K,L,M post_processing
    class N final_output
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