bam2fastq

bam2fastq converts sequencing reads from BAM (Binary Alignment/Map) files into FASTQ format for use in downstream genomic analyses.

Key Features:

• Read Extraction: Extracts sequencing reads from BAM files while preserving read-associated metadata.
• Format Conversion: Converts extracted reads into FASTQ format compatible with downstream bioinformatics tools and pipelines.
• Galaxy Integration: Interfaces with the Galaxy platform as an execution engine and communicates via the Galaxy API or the Bioblend library.
• Cluster Execution: Leverages computational resources on the Institut Pasteur cluster through its Galaxy integration.

Scientific Applications:

• Metagenomic Analysis: Provides FASTQ input enabling use with MetaGenSense for metagenomic data analysis.
• Phylogenetic Studies: Supplies FASTQ-formatted reads for phylogenetic workflows such as NGphylogeny.fr.
• General Genomic Research: Delivers raw sequencing reads in FASTQ format for a broad range of genomic research projects.

Methodology:

Operates by interfacing with the Galaxy platform as an execution engine, communicating with Galaxy via its API or the Bioblend library, and leveraging the Institut Pasteur cluster for computation.