fqconvert

fqconvert converts quality scores in FASTQ files to the Sanger format for compatibility with analyses and tools that require Sanger-encoded FASTQ.

Key Features:

• Quality Score Conversion: Transforms quality scores from various encodings into the Sanger quality-score format.
• FASTQ I/O: Accepts FASTQ files with diverse quality-scoring formats and produces FASTQ files with converted Sanger scores.
• Galaxy Integration: Operates within the Galaxy platform, including the Galaxy@Pasteur instance, to run as part of Galaxy workflows.
• Programmatic Execution: Supports execution via the Galaxy API or the Bioblend library and leverages the Institut Pasteur compute cluster for job execution.

Scientific Applications:

• Metagenomic Data Analysis (MetaGenSense): Provides quality-score standardization for metagenomic workflows launched through MetaGenSense.
• Metagenomic Analysis (Shaman): Ensures FASTQ quality-score compatibility for metagenomic analyses in Shaman, a SHiny application.
• Phylogenetic Studies (NGphylogeny.fr): Standardizes quality scores to support upstream processing for phylogenetic analyses on NGphylogeny.fr.

Methodology:

Accept FASTQ files with various quality-scoring encodings, apply score-mapping algorithms to convert scores to the Sanger format, and write output FASTQ files with converted quality scores.