software-overview

A complete analysis and visualization package

The Chromium Software Suite is a complete package for analyzing and visualizing the Linked-Read sequencing data type produced by our unique 10x GemCode Technology. The Chromium Software Suite supports our comprehensive suite of workflow solutions, including Chromium Single Cell 3′, Genome, and Exome Solutions.

Explore Demo

The Chromium Software Suite is a complete, turn-key analysis solution.

Building upon widely accepted aligners and variant callers, our Chromium Software Suite provides bioinformatics and analysis pipelines that specifically leverage the molecular barcoding of our 10x GemCode Technology to enable phasing and structural variant calling. Results are produced in standard file formats such as BAM, VCF and BEDPE, which can also be visualized in a new haplotype-aware genome browser called Loupe.

Barcode Processing
Alignment
10x Lariat
Variant Calling
Freebayes, GATK
Phasing
SV Calling
10x
Loupe
Visualization
BAM, VCF, BEDPE
File Formats
Standard Pipeline Stages
10x Genomics Stages

Barcode Processing
Alignment
STAR
Transcript Counting
Gene-Cell Matrix
Expression Analysis
10x
Loupe
Visualization
BAM,
Matrix
File Formats
Standard Pipeline Stages
10x Genomics Stages

Long range NGS analysis

Best practices pipelines enhanced with phasing and structural variant calling for turn-key analysis.

Rich visualization

Fully haplotype-aware genome browser for phased SNPs, indels, and structural rearrangements.

Open source informatics

Powerful, open developer tools for building high-throughput informatics pipelines.

Long Ranger

Long Ranger

A set of analysis pipelines that perform sample demultiplexing, barcode processing, alignment, quality control, variant calling, phasing, and structural variant calling.

Learn more
Loupe Genome Browser

Loupe Genome Browser

A haplotype-enabled genome browser and structural variant visualizer.

Learn more

Cell Ranger

Cell Ranger

A set of analysis pipelines that combine robust transcriptome alignment with cellular barcoding and rapidly generate expression profiles across tens of thousands of cells at once.

Learn more
Loupe Cell Browser

Loupe Cell Browser

A browser that features an array of techniques for dimensionality reduction and clustering for single cell analysis.

Coming Soon