reformat_fastq

reformat_fastq reformats FASTQ files to remove or handle space characters within sequencing reads from MiSeq and HiSeq systems, ensuring compatibility with downstream bioinformatics analyses.

Key Features:

• Data Compatibility: Detects and corrects space characters within FASTQ read sequences to produce files compatible with downstream tools that do not accept spaces in sequences.
• Sequencing System Support: Targets formatting issues specific to FASTQ files generated by MiSeq and HiSeq sequencing platforms.
• Integration with Galaxy@Pasteur: Integrated into the Galaxy@Pasteur instance to execute as part of Galaxy workflows on the Institut Pasteur compute infrastructure.
• Web Service Integration: Interfaces with Galaxy via its API or the Bioblend library as part of a suite of custom web services around the Galaxy@Pasteur instance.

Scientific Applications:

• Metagenomic Data Analysis: Provides properly formatted FASTQ input for automated metagenomic workflows and tools such as MetaGenSense.
• Phylogenetic Studies: Supplies correctly formatted reads for next-generation phylogenetic platforms such as NGphylogeny.fr.
• General Bioinformatics Workflows: Improves the reliability of genomics and related analyses that require well-formatted FASTQ data.

Methodology:

The tool parses FASTQ files to read entries, detects sequences containing space characters, and rewrites sequence entries without spaces or with appropriate modifications to maintain data integrity; it can be executed within Galaxy@Pasteur workflows via the Galaxy API/Bioblend.