OCTOPUS-toolkit

OCTOPUS-toolkit automates retrieval and processing of large-scale next-generation sequencing (NGS) datasets to produce aligned BAM and BigWig files for epigenomic and transcriptomic analyses.

Key Features:

• Automated Pipeline: Automates setup and execution by integrating Aspera, SRA Toolkit, FastQC, Trimmomatic, HISAT2, STAR, Samtools, and HOMER.
• Data Retrieval: Automatically retrieves original files from the Gene Expression Omnibus (GEO) for ChIP-seq, ATAC-seq, DNase-seq, MeDIP-seq, MNase-seq, and RNA-seq datasets.
• Data Processing: Processes retrieved files sequentially to generate BAM and BigWig output formats.
• Genome Compatibility: Supports genomes of Homo sapiens, Mus musculus, Canis lupus familiaris, Arabidopsis thaliana, Danio rerio, Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae.
• Advanced Analysis Capabilities: Enables meta-analyses of datasets, motif searches for DNA-binding proteins, and identification of differentially expressed genes or protein-binding sites.

Scientific Applications:

• Integrative epigenomics and transcriptomics: Facilitates systematic and integrative analysis of epigenomic and transcriptomic NGS big data.
• Gene regulation and comparative studies: Supports analysis of gene expression, regulatory elements, and genomic interactions across multiple model organisms.

Methodology:

Automated retrieval from GEO using Aspera and SRA Toolkit, integration of FastQC, Trimmomatic, HISAT2, STAR, Samtools, and HOMER, and sequential processing of files to produce BAM and BigWig files and enable motif and differential analyses.