Reusable, Modular, Automated

Bioinformatics Pipelines

Whether you're running standard analyses or building custom workflows from scratch, Foundry gives you flexible ways to design, run, and manage pipelines.

Choose the approach that fits your expertise and goals:

  • Run pre-built pipelines for common omics analyses

  • Use the drag-and-drop builder to create custom pipelines from modular processes

  • Import Nextflow® pipelines to run and manage them in Foundry

  • Build with code using the Python/R SDK or Foundry CLI

Every pipeline in Foundry is reproducible by design – with versioning, provenance, and collaboration built in.

DRAG AND DROP

Pipeline Creation

Foundry offers a continually growing library of pre-built pipelines and modular pipeline building blocks for analysis.

Launch ready-to-run pipelines for your critical omics workflows with just a few clicks. Or, use Foundry’s drag-and-drop builder to combine pipeline building blocks into any pipeline you need – no coding required.

Whether you want a validated pipeline or to construct a custom one, Foundry gives you a powerful foundation with reproducibility built in from the start.

Hundreds of Ready-Made Options on Foundry

Pre-Processing Modules

Designed to clean, filter, and trim raw sequencing reads, removing noise and inconsistencies using tools like Trimmomatic and Cutadapt.

Available on Foundry

  • Trimming

  • Quality Filtering

  • Sequential Mapping

Sequencing Analysis Pipelines

Encompasses comprehensive workflows for processing various types of sequencing data from raw reads to quantification and quality metrics.

Available on Foundry

Genomic Sequencing

  • WGS/WES

  • PacBio

  • LAAVA

Transcriptomic Sequencing

  • RNA-Seq

  • tRNA-Seq

  • Ribosome Profiling

  • RiboSeq pipeline

Epigenomics

  • ATAC-Seq

  • ChIP-Seq

  • Super Enhancer

Microbial and Metagenomic Analysis

  • Taxprofiler

  • Bacterial Assembly and Annotation

  • Phylogeny from Bacterial Sequences

  • 16S Pipeline

Targeted and Amplicon-Based Sequencing

  • AmpliSeq

  • NanoSeq

  • CRISPR Pipeline

Small RNA Pipelines

Via Foundry offers piRNA pipelines specifically designed for the analysis of small RNA data

Available on Foundry

  • smRNA-seq

  • smRNA-seq (nf-core)

  • tRNA-seq

  • piRNA-seq

Single Cell Pipelines & Analysis Modules

Facilitates the processing and in-depth analysis of single-cell RNA-sequencing data with features for quality control, clustering, and cell type annotation.

Available on Foundry

  • scRNA-Analysis

  • Cell Ranger Multi

  • Cell Ranger Count

  • Single Cell inDrop

  • Single Cell 10x

  • CellChat2 Pipeline

  • Souporcell

Functional Genomics Analysis

Enables researchers to assess the biological significance of gene sets and pathways by identifying enrichment in gene expression data. Applies machine learning for genomic variant prediction, drug discovery, and disease risk prediction.

Available on Foundry

  • nf-core pipelines

  • cutandrun

  • rnafusion

  • methylseq

Spectral Omics Analysis

Converts raw mass‑spectrometry data into high‑confidence, quantified features and annotated molecules.

Available on Foundry

  • Proteomics (DIA-NN)

  • Metabolomics

  • Lipidomics

  • Glycomics

Variant Calling Pipelines

End‑to‑end workflows for germline, somatic, and viral variant discovery—from QC and alignment to recalibration, calling, filtering, and annotation—producing analysis‑ready VCFs and cohort summaries.

Available on Foundry

  • GATK

  • Sarek

  • viralrecon

Downstream Analysis

Via Foundry applies a set of processes after the initial alignment or quantification steps in a bioinformatics pipeline. These analyses refine, interpret, or extract more biologically meaningful insights from raw output data.

Available on Foundry

  • DE Module

  • GSEA Module

Peak Calling Module

Identifies accessible chromatin regions and enriched binding sites in ATAC-Seq and ChIP-Seq data, with an option for generating consensus peak calls across multiple samples.

Available on Foundry

  • MACS2 Module

Quality Control Modules

Quality Control integrated into Via Foundry pipelines to assess and aggregate the quality of sequencing reads and identify outliers within datasets.

Available on Foundry

  • FastQC

  • RSeQC

  • Picard

  • MultiQC

Quantification Modules

Via Foundry estimates gene and isoform expression levels for RNA-Seq data, and quantify reads in peak regions for ATAC-Seq and ChIP-Seq, generating comprehensive count and TPM matrices.

Available on Foundry

  • RSEM

  • Kallisto

  • Salmon

  • featureCounts

Spatial Omics Analysis

Processes spatial transcriptomics and proteogenomics data into spot‑ or cell‑level expression matrices with image registration, segmentation, QC, and spatial statistics. Results are ready for interactive visualization and integration with single‑cell references for cell‑type mapping and neighborhood analyses.

Available on Foundry

  • Xenium

  • Visium

  • GeoMx

Alignment Modules

Align sequencing reads to reference genomes or transcripts for various omics data types.

Available on Foundry

  • HISAT2

  • Kallisto

  • Bowtie2

  • Salmon

  • STAR Module

  • RSEM Module

Visualization Modules

Provides interactive applications and tools to explore, analyze, and present diverse omics data results.

Available on Foundry

  • UCSC (bigWig) Genome Browser

  • Proteomics/metabolomics interactive tools

  • Differential Analysis Modules (DESeq2, edgeR, Limma, DEBrowser)

  • GSEA Explorer

  • Network Explorer

  • scViewer

  • CELLxGENE

  • iSEE

  • Other 3rd party visualization tools

Sample AI Models

Via Foundry integrates Machine Learning (ML) and Artificial Intelligence (AI) algorithms to automate data aggregation and analysis for identifying patterns, making predictions, and generating hypotheses in omics data, including applications in genomic variant prediction, drug discovery, personalized medicine, and disease risk prediction.

Available on Foundry

  • AlphaFold

  • Geneformer

  • BigMHC

And Many More

We're continually adding new modules, processes, and pipelines to Foundry as the science evolves.

Advanced tooling, more control

Code Your Own Pipelines

For experienced bioinformaticians who want full control, Foundry supports code-first pipeline development through our Python/R SDK and command-line interface (CLI). Whether you’re building custom logic, integrating with other systems, or simply prefer working in code, Foundry enables you to develop and manage pipelines with complete control.

Software Development Kit (SDK)

  • Programmatic access to pipeline logic in Python or R

  • Build, run, and monitor pipelines directly from code

  • Adjust parameters mid-run and push outputs back into Foundry

  • Everything is tracked: code, environment, parameters, and artifacts

Command Line Interface (CLI)

  • Launch and monitor pipelines from the terminal

  • Automate bulk jobs across samples or cohorts

  • Upload and download datasets and results with ease

  • Integrate with shell scripts, cron jobs, or workflow managers

Code-first doesn’t mean going it alone – Foundry makes sure even your most custom workflows remain reproducible and shareable.

Compatible with Nextflow Elevated by Foundry

Foundry is fully compatible with Nextflow, so you can easily incorporate nf-core pipelines and run them with minimal setup.

It’s the best of both worlds: you lose the complexity of configs, disconnected logging, and pipeline sprawl – and gain the infrastructure, visibility, and collaboration features that make pipelines truly reusable.

Run Nextflow Pipelines Without the Glue Code

  • Import and execute standard Nextflow pipelines

  • Adjust parameters, inputs, and containers directly in Foundry

  • Skip DSL2 config wrangling and homegrown run-tracking systems

Scale Pipelines Across Your Infrastructure

  • Run jobs seamlessly on AWS, GCP, or HPC

  • Launch large-scale analyses without provisioning headaches

  • Monitor runs, inspect logs, and collect outputs in one place

Add Reproducibility and Metadata Context

  • Version tracking for every pipeline, module, and run

  • Strict containerization ensures consistent results every time

  • Monitor runs, inspect logs, and collect outputs in one place

Let's Get Started

Foundry unlocks the power of multi-omics data so you can generate extraordinary scientific insights.

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