[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill:01M6CZ3HZTYHZPNJQFQAC85AFH":3,"skill-same:01M6CZ3HZTYHZPNJQFQAC85AFH":95},{"skillNo":4,"name":5,"nameZh":6,"description":7,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":16,"categories":17,"keywords":18,"publishedAt":27,"linkOnly":28,"markdownContent":29,"markdownBody":30,"frontMatter":31,"refName":32,"commitSha":33,"skillDirectory":34,"forksCount":35,"repositoryHtmlUrl":36,"repositoryHomepageUrl":6,"ownerHtmlUrl":37,"ownerBlogUrl":6,"ownerDescription":6,"updatedAt":38,"install":39,"resources":52},"01M6CZ3HZTYHZPNJQFQAC85AFH","ngs-read-preprocessing",null,"Adapter trimming, quality filtering, and per-sample QC reporting with fastp.","Scientific-Tooling\u002Fstructured-intelligence","Scientific-Tooling","https:\u002F\u002Favatars.githubusercontent.com\u002Fu\u002F267453265?v=4","01M6CZ1SE6GGD4F67EAQ0PVX38","Scientific Tooling","01M6CZ1SJKCFVGH10Z3A152K02",4,"MIT","https:\u002F\u002Fgithub.com\u002FScientific-Tooling\u002Fstructured-intelligence\u002Fblob\u002Fmain\u002Fskills\u002Fngs-read-preprocessing\u002FSKILL.md",[],[19,20,21,22,23,24,25,26],"read","preprocessing","ngs read preprocessing","reporting","quality","filtering","quality filtering","sample","2026-11-10 10:12:30",false,"---\nname: ngs-read-preprocessing\ndescription: Adapter trimming, quality filtering, and per-sample QC reporting with fastp.\n---\n\n# Skill: ngs-read-preprocessing\n\n## Use When\n\n- The user wants to trim adapters from raw sequencing reads.\n- The user needs to filter low-quality reads or bases before downstream alignment.\n- The user wants to generate clean FASTQ files suitable for alignment or assembly.\n- The user needs a per-sample HTML QC report showing before\u002Fafter statistics.\n- The user wants to perform polyG or polyX tail trimming for NextSeq\u002FNovaSeq platforms.\n- The user needs to apply minimum read length filtering after trimming.\n\n## Inputs\n\n- Required:\n  - Input FASTQ R1 (`-i FILE`) — single-end read file or forward reads for paired-end.\n- Optional:\n  - Input FASTQ R2 (`-I FILE`) — reverse reads for paired-end sequencing.\n  - `--outdir DIR` — Output directory (default: `fastp_results`).\n  - `--threads N` — Number of worker threads (default: 4).\n  - `--min-qual N` — Minimum qualified quality phred value for sliding window filtering (default: 15).\n  - `--min-len N` — Minimum read length after trimming (default: 36 bp).\n  - `--polyg` — Enable polyG tail trimming (recommended for NextSeq\u002FNovaSeq two-color chemistry).\n  - Adapter sequences — auto-detected by default; user may supply explicit sequences via additional fastp flags.\n  - Additional fastp flags passed through as extra arguments.\n\n## Workflow\n\n1. Validate that input FASTQ files exist and are readable.\n2. Detect single-end vs. paired-end mode from the provided inputs (`-i` only vs. `-i` and `-I`).\n3. Run fastp with adapter auto-detection (or user-specified adapter sequences if provided).\n4. Apply quality filtering using a sliding window approach (default: Q15 qualified quality threshold).\n5. Apply length filtering to discard reads shorter than the minimum length (default: 36 bp).\n6. Enable polyG tail trimming for NextSeq\u002FNovaSeq platforms if `--polyg` is specified.\n7. Generate an HTML report and JSON statistics file with detailed before\u002Fafter metrics.\n8. Report summary: reads before\u002Fafter filtering, bases before\u002Fafter, Q20\u002FQ30 rates, and adapter trimming rate.\n\n## Output Contract\n\n- **Cleaned FASTQ file(s)** — Trimmed and filtered reads (`\u003Csample>_trimmed.fastq.gz`; R1 and R2 for paired-end).\n- **fastp HTML report** — Per-sample visual QC summary (`\u003Csample>_fastp.html`).\n- **fastp JSON report** — Machine-readable statistics (`\u003Csample>_fastp.json`).\n- **Summary statistics** — Reads in\u002Fout, bases in\u002Fout, Q20\u002FQ30 rates before and after filtering, adapter detection\u002Ftrimming rate.\n\n## Limits\n\n- fastp must be installed and available on `$PATH`.\n- fastp is single-threaded by default; use `-w` \u002F `--threads` to enable multi-threading (up to 16 threads).\n- This skill does not perform read alignment; use `genome-read-alignment` or `rnaseq-read-alignment` for that purpose.\n- This skill does not aggregate QC across multiple samples; use `ngs-quality-control` for multi-sample QC aggregation with MultiQC.\n- UMI processing is supported by fastp but is not enabled by default; pass `--umi` and related flags as extra arguments if needed.\n- Interleaved FASTQ input is not supported by the wrapper script; use fastp directly for interleaved input.\n- Common failure cases:\n  - Paired-end FASTQ files with mismatched read counts causing fastp to abort.\n  - Incorrect adapter sequences provided, leading to untrimmed reads.\n  - Disk full during output writing, producing truncated FASTQ files.\n","# Skill: ngs-read-preprocessing\n\n## Use When\n\n- The user wants to trim adapters from raw sequencing reads.\n- The user needs to filter low-quality reads or bases before downstream alignment.\n- The user wants to generate clean FASTQ files suitable for alignment or assembly.\n- The user needs a per-sample HTML QC report showing before\u002Fafter statistics.\n- The user wants to perform polyG or polyX tail trimming for NextSeq\u002FNovaSeq platforms.\n- The user needs to apply minimum read length filtering after trimming.\n\n## Inputs\n\n- Required:\n  - Input FASTQ R1 (`-i FILE`) — single-end read file or forward reads for paired-end.\n- Optional:\n  - Input FASTQ R2 (`-I FILE`) — reverse reads for paired-end sequencing.\n  - `--outdir DIR` — Output directory (default: `fastp_results`).\n  - `--threads N` — Number of worker threads (default: 4).\n  - `--min-qual N` — Minimum qualified quality phred value for sliding window filtering (default: 15).\n  - `--min-len N` — Minimum read length after trimming (default: 36 bp).\n  - `--polyg` — Enable polyG tail trimming (recommended for NextSeq\u002FNovaSeq two-color chemistry).\n  - Adapter sequences — auto-detected by default; user may supply explicit sequences via additional fastp flags.\n  - Additional fastp flags passed through as extra arguments.\n\n## Workflow\n\n1. Validate that input FASTQ files exist and are readable.\n2. Detect single-end vs. paired-end mode from the provided inputs (`-i` only vs. `-i` and `-I`).\n3. Run fastp with adapter auto-detection (or user-specified adapter sequences if provided).\n4. Apply quality filtering using a sliding window approach (default: Q15 qualified quality threshold).\n5. Apply length filtering to discard reads shorter than the minimum length (default: 36 bp).\n6. Enable polyG tail trimming for NextSeq\u002FNovaSeq platforms if `--polyg` is specified.\n7. Generate an HTML report and JSON statistics file with detailed before\u002Fafter metrics.\n8. Report summary: reads before\u002Fafter filtering, bases before\u002Fafter, Q20\u002FQ30 rates, and adapter trimming rate.\n\n## Output Contract\n\n- **Cleaned FASTQ file(s)** — Trimmed and filtered reads (`\u003Csample>_trimmed.fastq.gz`; R1 and R2 for paired-end).\n- **fastp HTML report** — Per-sample visual QC summary (`\u003Csample>_fastp.html`).\n- **fastp JSON report** — Machine-readable statistics (`\u003Csample>_fastp.json`).\n- **Summary statistics** — Reads in\u002Fout, bases in\u002Fout, Q20\u002FQ30 rates before and after filtering, adapter detection\u002Ftrimming rate.\n\n## Limits\n\n- fastp must be installed and available on `$PATH`.\n- fastp is single-threaded by default; use `-w` \u002F `--threads` to enable multi-threading (up to 16 threads).\n- This skill does not perform read alignment; use `genome-read-alignment` or `rnaseq-read-alignment` for that purpose.\n- This skill does not aggregate QC across multiple samples; use `ngs-quality-control` for multi-sample QC 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