iKARAJ

iKARAJ automates retrieval of genomic and transcriptomic sequence data, associated metadata, and supplementary files from PMCIDs, publication URLs, and accession numbers to support genomics and transcriptomics analyses.

Key Features:

• Automated Data Querying: Accepts PMCIDs (PubMed Central Identifiers), publication URLs, and accession numbers to locate datasets referenced in publications.
• Diverse File Format Retrieval: Automates querying and downloading of genomic and transcriptomic sequence files in diverse file formats.
• Dataset Summary and Selection: Generates a summary list of accessible datasets that were generated by or used in the specified scientific articles.
• Disk Space Management: Calculates the total size of selected files and verifies availability of local disk space prior to download.
• Metadata Table Generation: Creates comprehensive metadata tables including sample information and experimental design for each dataset.
• Supplementary Data Downloading: Downloads supplementary data tables attached to publications.
• Parallel Downloading Framework: Uses Aspera Connect to perform parallel downloads of large datasets.

Scientific Applications:

• Genomics studies: Acquisition of genomic sequence datasets and associated metadata to support genomic analyses.
• Transcriptomics studies: Collection of transcriptomic sequence datasets and associated metadata for transcriptomic analyses.
• Data reuse and reanalysis: Retrieval of supplementary tables and metadata to enable reanalysis and integration of published datasets.

Methodology:

Accepts PMCIDs, publication URLs, and accession numbers; queries publication and accession records to identify accessible genomic and transcriptomic datasets and associated file formats; generates dataset summaries and metadata tables with sample and experimental-design information; calculates total download size and checks local disk space; downloads supplementary data tables; and performs parallel downloads using Aspera Connect.