Foundry Processes
Foundry Processes are the reusable building blocks that power Via Foundry pipelines. Each process captures a single, well-defined operation for alignment, quantification, quality control, reporting, and more, so that analyses are easy to compose, audit, and extend.
Use this index to explore the available process groups and dive into their detailed documentation.
Process Groups
- Alignment – genome and transcriptome alignment utilities.
- Annotation – ORF cataloguing, metadata, and annotation helpers.
- Assembly – genome/metagenome assembly workflows.
- Binning – metagenomic binning and refinement.
- Cell Type Mapper – reference-based cell type assignment.
- CellChat2 – cell–cell communication analysis modules.
- CRISPR – MAGeCK-based CRISPR screen support.
- Differential Expression – DESeq2/Limma post-processing.
- File Conversions – common format conversion utilities.
- Functional Profiling – HUMAnN and related profiling steps.
- GATK4 – best-practice germline and somatic variant callers.
- Gene Set Enrichment – GSEA preparation modules.
- HLA – OptiType HLA typing workflow.
- Index Building – reference index construction and validation.
- IRFinder – intron retention analysis.
- LAAVA – long-read AAV analysis components.
- MAG-QC – MAG quality control and summarisation.
- Miscellaneous – shared utilities and orchestration helpers.
- Pre-Processing – trimming, filtering, and FASTQ preparation.
- Quality Control – FastQC, MultiQC, Picard, and RSeQC steps.
- Ribosome Profiling – ribotricer-driven profiling support.
- Short Read Taxonomy – Kraken2, Bracken, and Metaphlan pipelines.
- Single Cell – Cell Ranger, pySCENIC, scVelo, and Seurat integrations.
- Spatial – Space Ranger and spatial data conversions.
- Summary – adapter, trimming, and coverage report collectors.
- TE Transcripts – transposable element quantification.
- Transcript Quantification – featureCounts, Salmon, Kallisto, RSEM.
- Tutorial – documentation-focused tutorial processes.
- UMInator – UMI-aware consensus generation modules.