Pipelines

For the following NGS technologies, computational pipelines were developed by BCF and are available for BCF users and projects. The pipelines are developed using dedicated tools, that allow to create reproducible and transferrable pipelines such as Nextflow [1] or Snakemake [2]. Please let us know if you are interested in a technology that is not listed so far.

For more information on Next generation sequencing and single cell sequencing please visit NGS background.

Bulk sequencing:

  • RNA-Seq
  • miRNA-Seq
  • ChIP-Seq
  • ATAC-Seq

Single cell sequencing:

  • 10x-RNA-Seq
  • 10x-ATAC-Seq
  • 10x-visum (spatial transcriptomics)
  • 10x-VDJ
  • 10x-Feature-Barcoding
  • Drop-Seq
  • Smart-Seq
  • sc-variant-calling

References
[1] https://www.nextflow.io
[2] https://snakemake.readthedocs.io/en/stable/