Essential tools we use
Below are curated links to widely used, open-source tools and communities we frequently integrate into NGS and genomics workflows. Open links in a new tab to view documentation and downloads.
A portable, reproducible workflow engine for building scalable bioinformatics pipelines (cloud & HPC).
Community-curated collection of production-grade Nextflow pipelines and best-practice templates.
Industry-standard toolkit for variant discovery and genotyping; widely used in germline and somatic workflows.
Variant Effect Predictor — annotation of variants with predicted consequences and links to population and clinical databases.
Core utilities for sequence alignment manipulation, variant file (VCF/BCF) handling and basic variant filtering.
Comprehensive R toolkit for single-cell RNA-seq analysis: preprocessing, integration, clustering, and visualization.
If you'd like, I can add short quick-start commands or links to specific nf-core pipelines (rnaseq, snakemake examples) that match your target assays.