Reusable, Modular, Automated

Bioinformatics Pipelines

Use the nocode drag-and-drop pipeline builder, build your own pipeline, or import an existing pipeline and edit as you go with Foundry SDK or Foundry CLI.

DRAG AND DROP

Pipeline Creation

Jump straight into the pipeline builder tool with a drag-and-drop graphical interface to rapidly build out pipelines with ready-made processes accessible on Foundry. Bioinformaticians at Via Scientific are regularly adding new processes to expand our library to save you time, effort, and resources.

Ready-Made Processes 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 Processes

  • 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 Processes

Genomic Sequencing

  • WGS/WES

  • PacBio

  • LAAVA

Transcriptomic Sequencing

  • RNA-Seq

  • tRNA-Seq

  • Ribosome Profiling

Epigenomic

  • ATAC-Seq

  • ChIP-seq

  • Super Enhancer

Microbial and Metagenomic Analysis

  • Ttaxprofiler

  • Bacterial Assembly and Annotation

  • Phylogeny from Bacterial Sequences

Targeted and Amplicon-Based Sequencing

  • Ampliseq

  • Nanoseq

Super Enhancer

tRNA-Seq

PacBio

LAAVA

Small RNA Pipelines

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

Available Processes

  • 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 Processes

  • scRNA-Analysis

  • Cell Ranger Multi

  • Cell Ranger Count

  • Single Cell inDrop

  • Single Cell 10x

  • Honeycomb scRNA-Seq

  • 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 Processes

  • nf-core pipelines

  • cutandrun

  • rnafusion

  • methylseq

Spectral Omics Analysis

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

Available Processes

  • 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 Processes

  • GATK

  • Sarek

  • viralrecon

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 Processes

  • 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 Processes

  • 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 Processes

  • 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 Processes

  • Xenium

  • Visium

  • GeoMX

Alignment Modules

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

Available Processes

  • HISAT2

  • Kallisto

  • Bowtie2

  • Salmon

Visualization Modules

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

Available Processes

  • UCSC (bigWig) genome browser

  • Proteomics/metabolomics interactive tools

  • Differential Analysis Modules (DEseq2, EdgeR, Limma, DEBrowser)

  • GSEA Explorer

  • Network Explorer

  • HoscViewerneycomb scRNA-Seq

  • 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 Processes

  • Alphafold

  • Colab

  • Geneformer

  • BigMHC

Advanced tooling, more control with

BYO Pipelines

Via Foundry makes it easy to build-your-own pipeline and edit existing pipelines for those who are experienced in bioinformatics. If you are a bioinformatician that wants to use particular tools or write your own code, we make it easy to get full control over each step and make tweaks as you go.

Software Development Kit (SDK)

Full scripting access to analysis workflows, available for both Python and R.

  • Access workflows, data, and results directly from code.

  • Build custom logic, adjust parameters mid‑run, and push artifacts back to your workspace.

  • Reproducible results with traceable session tracking that captures code, environment, and parameters.

Command Line Interface (CLI)

Terminal commands directly in Via Foundry for speed and automation.

  • Launch and monitor pipelines with a single command.

  • Upload/download datasets and results with ease.

  • Automate bulk processing by looping across samples or cohorts.

  • Integrate with your broader stack to use in shell scripts, cron jobs, or larger workflow orchestration.

Via Scientific Workbench

Launch your favorite environments like JupyterLab or RStudio, fully configured in the cloud.

  • Write and execute custom code for exploratory and interactive work.

  • Transform, explore, and visualize results, then feed outputs back into pipelines.

  • Configure CPU cores, RAM, and GPUs each session to keep a grip on budget and calculation speed.

  • Robust data mounting in hosted applications, such as JupyterLab and RStudio.

Built on Nextflow
‍Elevated by Foundry

Bring your own Nextflow

Import nf‑core or standard Nextflow pipelines and run them directly in Foundry.

Simplify Pipeline Management

Via Foundry's graphical user interface makes it easier to create and update complex pipelines with less effort, and Nextflow’s modular structure provides flexibility plus agility.

Streamline Execution

The platform enables the analysis and management of large quantities of samples across High-Performance Computing (HPC) environments, cloud services like AWS and Google Cloud, or personal workstations.

Reproduce Results

Via Foundry ensures reproducible pipelines with version tracking, and you can modify parameters for different attempts to view results for multiple attempts in a run.

Let's Get Started

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

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