Is this suitable for researchers without bioinformatics training?

Yes, it is specifically designed to guide bench scientists through the technical steps of pipeline deployment, environment checking, and data configuration using a clear checklist.

Can I use this with public datasets from NCBI?

Yes, the skill includes specialized scripts to fetch study info and download FASTQ files directly from GEO and SRA accessions using GSE, GSM, or SRR IDs.

What pipelines are supported by this skill?

The skill currently supports nf-core/rnaseq for gene expression analysis, nf-core/sarek for variant calling (WGS/WES), and nf-core/atacseq for chromatin accessibility analysis.

How does the skill handle samplesheet creation?

It provides automated scripts that discover your FASTQ/BAM files, pair R1/R2 reads, infer metadata, and validate the CSV format required by specific nf-core pipelines.

Do I need to install all bioinformatics tools manually?

No, the skill relies on Nextflow and Docker (or Singularity) to manage software dependencies automatically through containers, ensuring a clean and reproducible environment.

Nextflow Bioinformatics Pipelines

Name: Nextflow Bioinformatics Pipelines
Author: anthropics

byanthropics

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147

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Data Science & ML

Automates the deployment and execution of nf-core bioinformatics pipelines for genomics, transcriptomics, and epigenomics data analysis.

This skill empowers researchers and bench scientists to run sophisticated nf-core bioinformatics pipelines, including rnaseq, sarek, and atacseq, without needing deep command-line expertise. It handles the end-to-end workflow from acquiring public datasets from GEO/SRA and validating local environments to generating samplesheets and executing large-scale omics analyses using Docker or Singularity. By providing standardized implementation patterns and automated checks, it ensures reproducible and robust biological data processing for gene expression, variant calling, and chromatin accessibility studies.

Key Features

01Intelligent samplesheet generation and validation for local sequencing files

02Automated nf-core pipeline selection for RNA-seq, WGS/WES, and ATAC-seq

03Comprehensive environment validation for Docker, Nextflow, and Java requirements

04147 GitHub stars

05Built-in support for standardized reference genomes and iGenomes integration

06Direct acquisition and processing of public data from GEO and SRA accessions

Use Cases

01Performing variant calling on whole genome or exome sequencing datasets using Sarek

02Processing public GEO datasets for chromatin accessibility research via ATAC-seq

03Analyzing RNA-seq data to determine differential gene expression from local FASTQs

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add anthropics/life-sciences nextflow-development

For use in Claude.ai and ChatGPT

Download Skill