fastqrepair

What problem does it solve?

This Skill automates the recovery and cleanup of damaged or noncompliant FASTQ data so sequencing runs can continue with valid reads and reliable quality control.

Core Features & Use Cases

• FASTQ Recovery and Repair: Fixes corrupted FASTQ.gz files, removes invalid reads, and restores read pairing when possible.
• Sequencing Workflow Automation: Runs the nf-core/fastqrepair pipeline with a samplesheet, required inputs, and reproducible output organization.
• Quality Reporting: Produces cleaned FASTQ outputs, pipeline metadata, and MultiQC reports for downstream analysis and review.
• Use Case: A bioinformatics analyst can take a messy paired-end sequencing dataset, repair the reads, and deliver a validated result set for the next pipeline stage.

Quick Start

Ask the assistant to run the fastqrepair pipeline on your samplesheet and save the cleaned outputs to your chosen results directory.