building-genomics-pipelines

This skill should be used when the user asks to "build a genomics pipeline", "call variants", "analyze RNA-seq", "run ChIP-seq analysis", "annotate variants", "QC sequencing data", "detect CNVs", or when writing any bioinformatics pipeline code involving NGS data. Provides expert guidance on pipeline frameworks (Nextflow, Snakemake, WDL), alignment, variant calling, and production-ready nf-core workflows.

1.13x

Quality

—

Does it follow best practices?

Impact

78%

1.13x

Average score across 3 eval scenarios

Securityby

Advisory

Suggest reviewing before use

Evaluation results

74%

18%

Bulk RNA-seq Analysis Pipeline Setup

RNA-seq pipeline with nf-core, DESeq2, QC

Criteria

Without context

With context

Nextflow framework

nf-core/rnaseq

STAR aligner specified

100%

Salmon quantification

87%

GRCh38 reference

100%

Docker/Singularity profile

100%

87%

Samplesheet format

50%

100%

FASTQ naming convention

100%

DESeq2 for DE analysis

100%

tximport for Salmon import

100%

LFC shrinkage applied

100%

MultiQC mentioned

100%

80%

11%

Germline Variant Discovery and Annotation Pipeline

Germline calling, VEP annotation, rare disease filtering

Criteria

Without context

With context

DeepVariant for germline calling

VEP as primary annotator

100%

Variant normalization before annotation

100%

bgzip + tabix indexing

100%

VEP functional prediction plugins

100%

CRAM over BAM

gnomAD AF filter

62%

100%

IMPACT filter

100%

PASS filter applied

100%

Containerization mentioned

100%

MultiQC or staged QC

75%

100%

Indexed output files

100%

82%

Somatic Mutation and Structural Variant Analysis for Tumor Genomics

Somatic variants, Manta+GRIDSS SV calling, AnnotSV

Criteria

Without context

With context

Mutect2 for somatic SNVs

100%

Manta for SV calling

100%

GRIDSS for complex SVs

100%

Multi-caller SV merging

100%

AnnotSV for SV annotation

100%

bgzip + tabix for VCF outputs

100%

nf-core/sarek awareness

CRAM preference noted

Tumor/normal pair mode

100%

SV size filter applied

100%

Quality-based SV filtering

100%

Containerization mentioned

Repository: provectus/awos-recruitment
Commit: 4596913

Evaluated: 14 days ago
Agent: Claude Code
Model: Claude Sonnet 4.6

Table of Contents

Bulk RNA-seq Analysis Pipeline Setup Germline Variant Discovery and Annotation Pipeline Somatic Mutation and Structural Variant Analysis for Tumor Genomics

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