Pipeline Store

Curated bioinformatics pipelines

Browse study-scale analysis workflows and order-scoped sequencing utilities available in SeqDesk.

Pipeline Store

Available Pipelines

Study pipelines run across complete studies, while order pipelines operate on individual order samples and their linked sequencing files.

Study pipelines

Study pipelines run across a whole study and combine multiple samples for larger analysis, reporting, and data upload or submission workflows.

v3.0.0Study pipelinemetagenomics

MAG Pipeline

nf-core/mag

Metagenome assembly, binning, and QC in one workflow.

assemblybinningqc
v1.0.0Study pipelinesubmission

SubMG Submission

submg

Prepare and submit reads, assemblies, and bins to ENA.

enasubmissionmetadata
v0.1.0Study pipelinemetagenomics

MetaxPath

MetaxPath

Private long-read pathogen profiling workflow.

Private license required