FASTQ Preprocessing with fastp
Preprocesses Illumina FASTQ sequencing reads with automated adapter trimming, quality filtering, and interactive QC reporting in a single high-speed pass.
FASTQ Preprocessing with fastp guides Claude Code in executing ultra-fast quality control and adapter trimming for high-throughput sequencing data across RNA-seq, WGS, WES, ChIP-seq, and ATAC-seq pipelines. Operating 3–10x faster than traditional tools like Trim Galore and Trimmomatic, fastp automatically detects Illumina adapters via paired-end overlaps, repairs mismatched base calls in overlap regions, trims polyX/polyA tails, and applies rigorous Phred-score quality and length filtering. The skill provides interactive interview templates, ready-to-run shell pipelines, and Python parsing scripts for both HTML and machine-readable JSON QC outputs to enforce automated quality gates prior to alignment with STAR, BWA-MEM2, or Salmon.