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fastq-analysis-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

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**: `re….

OpenClawNanoClawAnalysisReproductionfastq-analysis🧬 bioinformatics (gptomics bio-* suite)bioinformatics tools & pipelinesguide

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/fastq-analysis

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • 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).

Source Doc

Excerpt From SKILL.md

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.

Use cases

  • Use fastq-analysis-pipeline for single-cell or spatial omics analysis.
  • Apply fastq-analysis-pipeline to clustering, integration, or trajectory workflows.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

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