Singleron developed its own bioinformatic software CeleScope®, to process the data generated by SCOPE-chip®. These pipelines take paired-end FASTQ files as input and generate output files which can be used for downstream data analysis as well as a summary of QC criteria.
Currently, CeleScope® includes the following pipelines:
celescope rna for single-cell RNA-seq data generated with GEXSCOPE kits. It performs preprocessing, genome alignment, feature counting, expression matrix generation, clustering, marker gene expression analysis and cell type assignment (optional).
celescope vdj for single-cell Immune Repertoire data generated with GEXSCOPE VDJ kits. It performs preprocessing, UMI consensus, vdj sequence alignment, UMI filtering and clonetypes counting.
celescope tag for single-cell Multiplexing data generated with CLindex Sample Multiplexing kits. It performs preprocessing, tag counting, tag assignment and multiplets identification.
celescope dynaseq for single-cell dynamic transcriptome data generated with DynaSCOPE kits. It performs preprocessing, genome alignment, feature counting, expression matrix generation, clustering, nucleotide substitution statistic and nascent RNA identification.
The software can be downloaded for free under Github.