fqcleaner

fqcleaner performs preprocessing of FASTQ files from high-throughput sequencing by trimming low-quality bases, filtering duplicate reads, and removing artefacts such as adapter sequences to produce cleaned data for downstream analyses.

Key Features:

• Quality Trimming: Removes low-quality bases from reads in FASTQ files to retain high-confidence sequence data.
• Duplicate Filtering: Identifies and removes duplicate reads to reduce redundancy introduced during sequencing.
• Artefact Removal: Detects and removes artefacts including adapter sequences and other non-biological contaminants.

Scientific Applications:

• Metagenomic Studies: Preprocesses FASTQ data for metagenomic analyses of microbial communities and integrates with platforms such as MetaGenSense.

Methodology:

Operates within the Galaxy framework using the Galaxy API and the Bioblend library to execute on the Institut Pasteur compute cluster.