fastp-fastq-preprocessing

What problem does it solve?

This Skill automates the essential preprocessing of raw FASTQ sequencing data, cleaning it by removing adapters and low-quality bases, which is crucial for downstream bioinformatics analysis.

Core Features & Use Cases

• Adapter Trimming: Automatically detects and removes Illumina adapters.
• Quality Filtering: Filters reads based on Phred quality scores and length.
• QC Reporting: Generates detailed HTML and JSON quality control reports.
• Use Case: Prepare raw RNA-seq FASTQ files for alignment by removing adapters and low-quality bases, ensuring cleaner data for gene expression analysis.

Quick Start

Run fastp to trim adapters and quality filter paired-end FASTQ files named 'sample_R1.fastq.gz' and 'sample_R2.fastq.gz', outputting to 'sample_R1.trimmed.fastq.gz' and 'sample_R2.trimmed.fastq.gz', and generate reports 'sample_qc.html' and 'sample_qc.json' using 8 threads.