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fastp-workflow

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Runs all-in-one FASTQ preprocessing with fastp in a single pass - adapter trimming via paired-end overlap analysis, quality/length filtering, 2-color poly-G removal, base correction, optional dedup/UMI/merge, and HTML/JSON reports. Use when preprocessing bulk Illumina data and wanting one fast tool instead of separate Cutadapt, Trimmomatic, and FastQC steps. For precise small-RNA/amplicon adapters use adapter-trimming; for molecule-accurate UMI dedup use umi-processing.

When to use

• Bulk PE WGS/WES/RNA/cfDNA preprocessing
• Adapter trimming via paired-end overlap analysis
• Quality and length filtering
• 2-color poly-G removal
• Base correction
• Optional dedup/UMI/merge
• HTML/JSON report generation

When not to use

• Precise small-RNA/amplicon adapters
• Molecule-accurate UMI dedup
• Transcriptome QC
• RNA-seq quantification dedup
• DNA coordinate dedup

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