fastq-analysis-pipeline
Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and single-cell RNA-seq workflows.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill fastq-analysis --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Overview OmicVerse provides a complete FASTQ-to-count-matrix pipeline via the `ov.alignment` module. This skill covers: - **SRA data acquisition**: `prefetch` and `fqdump` (fasterq-dump wrapper) - **Quality control**: `fastp` for adapter trimming and QC reports - **RNA-seq alignment**: `STAR` aligner with auto-index building - **Gene quantification**: `featureCount` (subread featureCounts wrapper) - **Single-cell path**: `ref` and `count` via kb-python (kallisto/bustools) - **Parallel SRA download**: `parallel_fastq_dump` All functions share a common CLI infrastructure (`_cli_utils.py`) that handles tool resolution, auto-installation via conda/mamba, parallel execution, and streaming output. ## Instructions 1. **Environment setup** - Bioinformatics tools are resolved automatically from PATH or the active conda environment. - If `auto_install=True` (default), missing tools are installed via mamba/conda on demand. - Supported tools: `prefetch`, `vdb-validate`, `fasterq-dump`, `fastp`, `STAR`, `samtools`, `featureCounts`, `pigz`, `gzip`. - For the single-cell path, ensure `kb-python` is installed: `pip install kb-python`. 2. **SRA data download** (`ov.alignment.prefetch` + `ov.alig
- Overview
- Instructions
- Critical API Reference
- Sample Format Convention
- Auto-installation
- Examples
- References
What does the fastq-analysis-pipeline skill do?
Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and single-cell RNA-seq workflows.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill fastq-analysis --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.