Start from the experiment you ran.

Each starter pipeline is the analysis a core facility would run for that kind of data, already connected, with the settings worth changing exposed.

INPUTFASTQQCfastpALIGNSTARQUANTSalmonSTATSDESeq2

RNA-seq

Find the genes that changed, the week the run finishes.

For bench scientists comparing conditions, timepoints or genotypes.

  • fastp
  • STAR or Salmon
  • DESeq2
  • Figures
See the pipeline
known sitesINPUTFASTQALIGNBWA-MEMVARIANTSGATKANNOTATEVEPREFknown.vcf

Genomics

Call and annotate variants without a cluster account.

For groups sequencing patient samples, model organisms or engineered lines.

  • BWA-MEM
  • GATK
  • VEP
See the pipeline
databaseINPUTmzMLPEAKSPeakPickQUANTFeatFinderIDProteinIDREFUniProt

Proteomics

From mass spec runs to identified proteins.

For labs running discovery proteomics alongside their other experiments.

  • Peak picking
  • Feature finding
  • Protein identification
See the pipeline
transcriptomeINPUTFASTQCOUNTCellRangerQCScanpyEMBEDUMAPREFGRCh38

Single-cell

Cluster your cells and find what makes each cluster different.

For groups profiling tissues, organoids or differentiation time courses.

  • Cell Ranger
  • Scanpy
  • UMAP
See the pipeline

Working with a different kind of data? Tell us what it is and we will build the starter for it.

Your experiment, already wired up.

OpenBionode is in early access. Tell us what you analyse and we’ll make sure the steps you need are ready when your seat opens.

Early access for research labs. No spam, just one note when your seat opens.