solid2fastq

solid2fastq converts SOLiD (Sequencing by Oligonucleotide Ligation and Detection) output files into FASTQ format for compatibility with standard downstream sequencing analysis pipelines.

Key Features:

• Format Conversion: Translates raw SOLiD output files into FASTQ format to enable use with FASTQ-based analysis tools.
• Galaxy@Pasteur integration: Runs within the Galaxy@Pasteur computational framework to perform conversions in that environment.
• High-throughput processing: Supports high-throughput conversion workflows on the Institut Pasteur cluster infrastructure.
• Programmatic execution: Utilizes Galaxy's API and the Bioblend Python library to programmatically execute conversion tasks.

Scientific Applications:

• Genomic sequencing: Facilitates analysis of genomic sequences generated on SOLiD platforms by providing FASTQ-formatted reads.
• Metagenomic studies: Enables SOLiD-derived metagenomic datasets to be processed with FASTQ-compatible tools such as MetaGenSense.
• Phylogenetic analysis: Supports phylogenetic workflows by providing FASTQ input compatible with services like NGphylogeny.fr.

Methodology:

Operates within the Galaxy@Pasteur framework, utilizing Galaxy's API and the Bioblend library to execute conversion tasks on the Institut Pasteur cluster.