Each pipeline below shows what data goes in, what every step does, and what comes back. Share a pipeline page with a colleague or a core facility to show exactly what a run produces.
5 pipelines available in Horizon today
Reconstruct T-cell receptors from paired-end bulk reads with TRUST4, then review clonotypes, productive receptors, and quality reports in one place.
Input
Raw paired-end FASTQ reads
Output
TCR tables, a repertoire summary, and a MultiQC report
Quantify gene and isoform expression from paired-end bulk reads with exon-aware alignment and quasi-alignment, ending in count tables and one quality report.
Input
Raw paired-end FASTQ reads
Output
Count tables, Salmon quant files, BAMs, and a MultiQC report
From 10x Genomics reads to an annotated, analysis-ready Seurat object: alignment, QC gating, integration, clustering, automated cell-type labels, and differential expression in one run.
Input
Raw paired-end 10x Genomics FASTQ reads
Output
Annotated Seurat object, H5AD, DGE tables, and reports
Quality checks and resource recommendations for any assay: FastQC on every sample, plus chemistry detection, preliminary cell-quality metrics, and strandedness calls for single-cell and bulk RNA-seq.
Input
Raw FASTQ reads
Output
FastQC reports, resource recommendations, and a MultiQC report
Turn a differential expression result into biological meaning: GO, KEGG and Reactome enrichment, GSEA on the ranked gene list, enrichment plots, and one HTML report per comparison.
Input
A DESeq2-based DGE table per comparison
Output
GO, KEGG and Reactome tables, GSEA results, plots, and an HTML report
Guides and related workflows
Short guides to the workflows we support, useful when deciding what you want from a run.
Talk with our team about building or adapting a workflow for your research, including deployment in your AWS environment.
Contact the team