extract_archive_merge

extract_archive_merge extracts and merges compressed archive files (zip, gz, tar.gz, fastq.gz, fastq.bz2, tar.bz2) into a single output to prepare genomic and metagenomic sequencing data for downstream analysis.

Key Features:

• File Format Support: Supports decompression of zip, gz, tar.gz, fastq.gz, fastq.bz2, and tar.bz2 archive formats.
• Decompression and Merging: Extracts archive contents and concatenates contained files into a single unified dataset.
• Galaxy@Pasteur integration: Executes within the Galaxy@Pasteur instance and can run on the Institut Pasteur compute cluster.
• API and Bioblend support: Interfaces with Galaxy via the Galaxy API or the Bioblend library for task submission and control.

Scientific Applications:

• Genomic data preprocessing: Converts compressed sequencing files into a single merged file for downstream bioinformatics analysis.
• Metagenomic studies: Prepares compressed metagenomic FASTQ archives for aggregate analysis.
• Phylogenetic analyses: Produces unified sequence datasets from archived files for phylogenetic workflows.

Methodology:

Identifies the compressed file format, applies the corresponding decompression algorithm to extract contents, and merges all extracted files into a single output; this process is automated within the Galaxy platform.