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.


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.


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.

Linked-Read Data Analysis Tools



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

ABySS 2.0

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


Software tools for haplotype assembly from sequence data

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.


Graphical assessment of structural variants using 10x Genomics data.

Linked-Read Simulator


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



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.