skills.rest
omicverse
omicverseOFFICIAL
Explore all skills by this author →
WebsiteGitHub

fastq-analysis-pipeline

Produce aligned BAM files and gene count matrices from SRA or FASTQ inputs.

32|5|Updated Mar 12, 2026
Search Tags:#alignment#rna-seq#star#fastq#featurecounts#sra#kb-python
One-click install
npx skills add https://github.com/omicverse/omicclaw --skill fastq-analysis-pipeline-omicverse
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: fastq-analysis-pipeline
Source: https://github.com/omicverse/omicclaw/tree/main/src/omicverse_skills/skills/fastq-analysis
Command: npx skills add https://github.com/omicverse/omicclaw --skill fastq-analysis-pipeline-omicverse

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This skill automates the end-to-end conversion of raw sequencing accessions or FASTQ files into aligned BAMs and gene count matrices, removing manual orchestration of downloads, QC, alignment, and quantification steps.

Core Features & Use Cases

  • SRA acquisition and conversion: Reliable SRA prefetch and fastq conversion with integrity checks and retry logic for network failures.
  • FASTQ quality control: Adapter trimming and QC report generation using fastp for single-end and paired-end reads.
  • Alignment and quantification: STAR alignment with auto-index building and featureCounts-based gene quantification for bulk RNA-seq.
  • Single-cell support: Reference building and quantification via kb-python (kallisto|bustools) with outputs in h5ad/loom/MTX formats.
  • Operational robustness: Auto-install missing tools via conda/mamba, parallel job execution, gzip handling, output skipping when files exist, and error-recovery options.
  • Typical use cases: Bulk RNA-seq from SRA to count matrix, one-click 10x v3 single-cell quantification, and local FASTQ processing pipelines.

Quick Start

Run a full RNA-seq workflow by sequentially invoking prefetch, fqdump, fastp, STAR, and featureCount (or use ref and count for single-cell) to produce a gene counts matrix.

Frequently Asked Questions about fastq-analysis-pipeline

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I process raw SRA accessions into a gene count matrix for bulk RNA-seq?▼

To generate a gene count matrix from SRA accessions, you sequentially run prefetch, fastq-dump, fastp for QC trimming, STAR alignment, and featureCounts quantification. This automation handles downloads, quality control, and alignment to produce the final counts.

Can I use STAR for alignment if I don't have a pre-built genome index?▼

Yes, STAR alignment supports auto-index building. The pipeline automatically builds the required genome index before alignment, eliminating the need to manually prepare a STAR index prior to processing your FASTQ files.

What is the best way to quantify single-cell RNA-seq FASTQ files into h5ad or loom formats?▼

For single-cell RNA-seq quantification, use kb-python (kallisto|bustools) to build references and count reads. This process outputs matrices directly into h5ad, loom, or MTX formats from local FASTQ inputs.

Do I need to manually install bioinformatics tools like fastp and STAR before running the pipeline?▼

No, manual installation of tools like fastp and STAR is not required. The pipeline supports auto-installation of missing bioinformatics dependencies via conda or mamba, handling environment setup automatically.

Does the RNA-seq pipeline support parallel execution and gzip streaming for large FASTQ files?▼

Yes, the RNA-seq pipeline supports parallel job execution, configurable threads and memory, and gzip streaming. It also skips existing output files to provide error-recovery and operational robustness for large datasets.

Related Skills

Explore More Education & Research Skills→
kiryteokiryteo
1

nextflow-development

Automate nf-core pipeline execution for RNA-seq, WGS/WES, and ATAC-seq data.

Community
Intermediate
ilove323ilove323

scvi-tools

Integrate and analyze single-cell genomics data with scvi-tools pipelines.

Community
Advanced
ClawBioClawBio
1.1k

seq-wrangler

Automate QC, trimming, alignment, and BAM processing for sequencing data.

Official
Intermediate
zongtingweizongtingwei
25

rna-quantification

Quantify gene and transcript abundances from RNA-seq reads using salmon, kallisto, or featureCounts.

Community
Advanced