tar.gz compression

Download for Linux 64-bit (tar.gz)

tar.xz compression

Download for Linux 64-bit (tar.xz)

Users can now perform automated cell type annotations using Gene Expression libraries.

Includes anonymized telemetry data collection to help 10x Genomics improve product functionality.

Strand information is now included in the `fragments.tsv` file.

Improvements to computational performance.

Cell Ranger ARC v2.1.0 highlights

To set up and run Cell Ranger ARC on Linux, please follow the steps below, or skip download and installation and get started with 10x Cloud Analysis:

<Grid style={{
  gap: '2rem'
}}><Anchor href={'/support/software/cell-ranger-arc/downloads/ref-build-steps'} style={{
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  }}> <Text as={'p'} color={'inherit'} size={'small'} weight={'medium'}>Steps to build references </Text> <Icon source={'nav-right'} color={'inherit'} size={'9px'} yPos={'1px'} /></Anchor> <Anchor href={'/support/software/cell-ranger-arc/latest/release-notes/reference-release-notes'} style={{
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  }}> <Text as={'span'} color={'inherit'} size={'small'} weight={'medium'}> 2020-A references & reference release notes</Text><Icon source={'nav-right'} color={'inherit'} size={'9px'} yPos={'1px'} /> </Anchor><DownloadLinkList softwareSlug={'cell-ranger-arc'} eula={false} downloadLinks={[{
    subtitle: 'Human reference (GRCh38) - 2024-A',
    fileSizeKB: 14000000,
    md5Sum: '57a41ecf38b1ec2ef66b3d345ad05839',
    title: 'Download Human Reference',
    summary: ['Human reference (GRCh38) dataset required for Cell Ranger ARC.'],
    batch: true,
    url: 'https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-GRCh38-2024-A.tar.gz'
  }, {
    subtitle: 'Mouse reference (GRCm39) - 2024-A',
    fileSizeKB: 13000000,
    md5Sum: '25c52a830d5f749558f84e1400c71486',
    title: 'Download Mouse Reference',
    summary: ['Mouse reference (mm10) dataset required for Cell Ranger ARC.'],
    batch: true,
    url: 'https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-GRCm39-2024-A.tar.gz'
  }]} /></Grid>

References

Cell Ranger ARC

Download Cell Ranger ARC

New: 2024-A reference transcriptomes now available for human and mouse

New feature: wavelet-based peak caller to improve detection of cluster-specific peaks

Improvements to duplicate marking algorithm

Improvements to computational performance: ~4x faster, 0.5x disk requirements

Cell Ranger ARC 2.0.2 highlights

Cell Ranger ARC is an advanced analytical suite designed for the Chromium Single Cell Multiome ATAC + Gene Expression sequencing. It provides in-depth analysis of gene expression and chromatin accessibility at a single cell level, uniquely linking these aspects for enhanced genomic understanding.

Overview

Getting Started

Download Center

Analysis

Tutorials

Algorithms

Advanced

Troubleshooting

Release Notes

Datasets

Loupe Browser

A tutorial on using Cell Ranger ARC mkref to create a reference for Rattus norvegicus

Custom Reference for Rat

Understand pipeline telemetry data collection and learn how to disable it if needed

Cell Ranger ARC Pipeline Telemetry

Learn more about input files required to run Cell Ranger ARC

Inputs

Generating FASTQs (mkfastq)

Specifying FASTQs

FASTQs with Illumina Software

Custom Reference (mkref)

Learn more about how to run Cell Ranger ARC

Running Pipelines

Command Line Arguments

Analyzing GEX + ATAC (count)

Aggregating Multiple Samples (aggr)

Custom Analysis (reanalyze)

Cell Type Annotation

Learn more about the output files generated by Cell Ranger

Outputs

Web Summary

Secondary Analysis

Feature-Barcode Matrices

Summary CSV

Per Barcode QC Metrics

ATAC Barcoded BAM

ATAC Fragments

ATAC Peaks

ATAC Peak Annotations

ATAC Transposition Counts

GEX Barcoded BAM

GEX Molecule Info (H5)

HDF5 Feature Barcode Matrix Format

Cell Type Annotations

What is Cell Ranger ARC?

<Flex style={{
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}}><div><Text as={'span'} size={'small'} weight={'medium'}>{'Starting with v2.1, anonymized telemetry data is collected and sent to 10x Genomics. '}</Text><Anchor href={'https://www.10xgenomics.com/support/software/cell-ranger-arc/latest/tutorials/cr-arc-pipeline-telemetry'}><Text as={'span'} color={'inherit'} size={'small'} weight={'medium'}>{'Learn how to disable.'}</Text></Anchor></div><Text as={'p'} size={'small'} weight={'medium'}>The cellranger-arc mkfastq pipeline is deprecated and will be removed in a future release. Please use Illumina’s BCL Convert to generate compatible FASTQ files.</Text></Flex>

We provide resources from protocols, user guides, and free-to-use analysis tools

Algorithms overview

Advanced pipeline content for Cell Ranger ARC.

View the latest updates to Cell Ranger ARC.

Browse Q&As from the 10x Genomics support team.

Access free public Chromium data from 10x Genomics.

Loupe Browser is a desktop application that allows you to interactively visualize data.

Previous Versions

Cell Ranger ARC 2.1.0 (Oct 6, 2025)

Cell Ranger ARC v2.1.0 highlights

Cell Ranger ARC 2.0.2 (Aug 18, 2022)

Cell Ranger ARC 2.0.2 highlights