Apr 27, 2017

Data analysis tools for single cell and Linked-Read applications

Shauna Clark

While we offer a robust set of software tools for 10x data visualization and analysis, including Long Ranger and Loupe, Cell Ranger and Loupe Cell Browser, and Supernova, we know there's always room for new and more specialized tools. Along with our 10x tools, a number of third-party software developers that have created their own computational tools for interpreting and analyzing 10x data*. There are a number of software options available for both Single Cell and Linked-Reads data.

Single Cell Data Analysis Tools


Web application that allows easy and intuitive exploration of gene expression to validate clustering, describe heterogeneity, and identify and discover new cell types in complex single cell transcriptome data sets.

  • Software Info
  • Preprint


R toolkit for single cell genomics and can be used to discover, classify, and interpret cell types and states from large-scale scRNA-seq datasets.

  • Software Info
  • Nature Webcast featuring Dr. Rahul Satija
  • Tutorial using 10x Chromium data


Toolkit for analyzing single-cell gene expression experiments. It performs differential expression analysis, and can find genes that differ between cell types or between cell states.

  • Publication
  • Nature Webcast featuring Dr. Cole Trapnell


SIMLR, (single-cell interpretation via multi-kernel learning), learns an appropriate cell-to-cell similarity metrics for dimension reduction and clustering of scRNA-seq data.

  • Publication
  • 10x Researcher Spotlight featuring Bo Wang

Linked-Read Data Analysis Tools



Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data.

  • Software Info
  • Preprint

ABySS 2.0

de novo sequence assembler intended for short paired-end reads and large genomes.

  • Software Info
  • Publication


Software tools for haplotype assembly from sequence data

  • Publication

Structural Variant Analysis


Genome-wide Reconstruction of Complex Structural Variants, or GROC-SVs, uses the long-fragment information from the 10x Genomics platform to identify structural variants, perform sequence assembly at the breakpoints, and reconstruct complex structural variants.

  • Preprint


Graphical assessment of structural variants using 10x Genomics data.

  • Preprint – coming soon
  • Michael Schatz AGBT 2017 Presentation

Linked-Read Simulator


Simulates whole genome sequencing using 10x Genomics Linked-Read technology.

  • Preprint
  • Michael Schatz AGBT 2017 Presentation



A set of light-weight command line tools for analyzing 10X genomics data. It is built to take care of low-level type operations in a 10x-specific way by accounting for the BX tag in 10x data


Utility functions for analyzing 10X Genomics data

*These tools are developed by the community and providing information in this blog does not imply endorsement by 10x Genomics.