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Attribute
Single-Cell & Spatial Biology

Cell Ranger

10x Genomics
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CategorySingle-Cell & Spatial Biology
Company10x Genomics
PriceFree to download for 10x Genomics data
StatusStatus not confirmed
AvailabilityAvailable on 10x Genomics support portal
Last checked20/09/2026
FeaturesDemultiplexing, barcode processing, and STAR alignment to reference genomes, Accurate cell-calling algorithms distinguishing intact cells from ambient RNA background, Support for 3' and 5' gene expression, immune profiling (VDJ), and feature barcoding, Automated web summary HTML reports with t-SNE/UMAP projections and sequencing QC metrics
Entry typeSoftware Pipeline
Access modeProprietary Freeware
AI roleDemultiplexing & Quality Filtering
Input dataNot recorded
Output dataNot recorded
Licence conditions10x Genomics End User License Agreement
Commercial eligibilityFree to download and use with 10x Genomics data
Compute requirements64GB+ RAM, 16+ CPU cores (HPC / Linux workstation)
ValidationNot recorded
TypeSingle-cell data processing pipeline
Intended useNot recorded
CompatibilityNot recorded
Manufacturer10x Genomics
Biological applicationSingle-cell RNA-seq, single-cell ATAC-seq, and immune repertoire profiling
Research workflowRaw Illumina BCL/FASTQ files -> aligned BAM and feature-barcode matrices
Evidence levelStandard protocol across thousands of published single-cell studies
Integration evidencehttps://www.10xgenomics.com/support/software/cell-ranger
Laboratory handoffMatrices feed directly into Scanpy, Seurat, or scvi-tools downstream analyses