Nextflow pipelines

We offer a range of sequencing processing pipelines. We develop them using Nextflow workflow language.

We run Nextflow pipelines on both Sanger LSF farm and on public Clouds using Netflow Tower.

Here is the list of the major pipelines we maintain and support:

  1. cellranger (for 10x data)

  2. cellranger (for CITEseq and HTO data)

  3. souporcell (for 10X data)

  4. ATAC-seq (for 10X and Smartseq2 data)

  5. velocyto (for 10X data)

  6. STARsolo (for 10X data)

  7. Bulk RNA-seq

  8. CellBender

  9. cell2location

  10. reprocessing public data

  11. Data Sharing - via S3 or Globus

  12. Image import to Omero Plus

  13. Uploading data to ArrayExpress FTPs


  • The pipelines listed above are our most commonly requested pipelines, if you want help with any other tool/software/pipeline then please get in touch and we will try to help you as best we can!

  • If you would like to run cellranger on samples sequenced at Sanger please put in a ticket for the NPG group by emailing new-seq-pipe [at] with the version of the cellranger and the genome you would like to use.

  • You can find a list of the current references we offer here: If you need a specific one we can build one for you, please reach out.