Ready for your all-in-one single cell sequencing solution?

From raw sequencing data to gene expression matrix

Sequencing data processing is the first step of single cell data analysis. CeleSCOPE® is a free analysis pipeline to process sequencing data and generate output files for downstream bioinformatics workflows.  

How CeleSCOPE® works

The input for  CeleSCOPE is paired-ended FASTQ files from sequencing.

 CeleSCOPE is a command-line tool that you can download and run locally.

The outputs for CeleSCOPE are the bam file and gene expression matrix files that allow you to perform downstream analysis

Software Download

CeleSCOPE is available for free from Github

User guide

Read the CeleSCOPE user guide to learn more about how to install and use the software

Supported Applications


Single cell and single nuclei sequencing data analysis


VDJ and full-length immuno receptor sequences

Transcriptome Dynamics

Time-resolved single cell sequencing data

Targeted Variant Detection

Sequencing data from whole transcriptome and SNPs, viral sequences, or fusion genes


Sequencing data obtained from multiplexed samples

Glycosylation Detection

Analysis of post-translational modification data in addition to single cell transcriptome


Analysis of bulk RNA sequencing data


RNA sequencing and surface protein expression data analysis


Check out our user guide at which provides a step-by-step walkthrough of the analysis pipeline.  

In addition, we run a regular bioinformatics bootcamp for beginners in single cell sequencing to bring them up-to-speed in running data analysis independently.

We do provide comprehensive single cell data analysis services from standard to advanced analysis. More information is available here.  

A Linux system with a minimum of 32GB RAM is required. Other than this, you’ll require sufficient disk space to store the input and output files which can be >500GB depending on the reference genome and sequencing depth. 

Yes, the output file from CeleSCOPE is compatible with all major single cell data analysis pipelines. Feel free to contact us if you need more support or information.  

Have a question?

Have a question?

Contact us if you have any questions regarding sequencing data processing or the CeleSCOPE software.