Public Pipelines
Via Foundry provides a continually expanding collection of public pipelines and sub-modules, ready to run in your environment. These cover a wide range of data types and analysis tasks.
Some of the pipelines and modules you can run in Foundry are:
Pre-processing Modules
- Trimming
- Quality filtering
- Sequential mapping
Sequencing Analysis Pipelines
- Whole-genome / whole-exome sequencing (WGS/WES)
- RNA-seq
- ATAC-seq
- ChIP-seq
- taxprofiler
- Bacterial assembly and annotation
- Phylogeny from bacterial sequences
- ampliseq
- nanoseq
- Super enhancer detection
- tRNA-seq
- Ribosome profiling
- Virus fitness pipeline using barcode analysis
- CRISPR analysis
Small RNA Pipelines
- smRNA-seq
- smRNA-seq (nf-core)
- tRNA-seq
- piRNA-seq
Single-Cell Pipelines & Analysis Modules
- scRNA analysis
- Cell Ranger Multi
- Cell Ranger Count
- Single-cell inDrop
- Single-cell 10x
- souporcell
Spectral Omics Analysis
- Proteomics
- Metabolomics
- Lipidomics
- Glycomics
Variant Calling Pipelines
- GATK
- Sarek
- viralrecon
Analysis Modules
Functional Genomics Analysis
- nf-core pipelines
- cutandrun
- rnafusion
- methylseq
Quality Control Modules
- LAAVA - Long-read AAV Analysis
- WF Clone Validation
- WF AAV QC
- FastQC
- RSeQC
- Picard
- MultiQC
Quantification Modules
- RSEM
- Salmon
- featureCounts
Spatial Omics Analysis
- Xenium / Visium
Alignment Modules
- HISAT2
- Kallisto
- Bowtie2
- Salmon
Visualization Modules
- UCSC genome browser (bigWig visualization)
- Proteomics / metabolomics interactive tools
- Differential analysis & visualization:
- DESeq2
- edgeR
- limma
- DEBrowser
- GSEA Explorer
- Network Explorer
- scViewer
- cellxgene
- iSEE
- Other third-party visualization tools
Sample AI Models
- AlphaFold
- Colab-based workflows
- Geneformer
- BigMHC