Data analysis tools for single cell and Linked-Read applications

Posted By: shauna-10x, on Apr 27, 2017 at 12:59 PM
0 Kudos

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. We've outlined them below and posted about them in the 10x Community Developers Network too.

 

Single Cell Data Analysis Tools

 

CellView

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.

Seurat

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.

Monocle

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

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

 

Assembly

ARCS

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.

HapCUT2

Software tools for haplotype assembly from sequence data

 

Structural Variant Analysis

GROC-SVs

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.

Topsorter

Graphical assessment of structural variants using 10x Genomics data.

 

Linked-Read Simulator

LRSIM

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

 

Miscellaneous

bxtools

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

 

tenx_utils

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.

2 Comments

Posted By: shauna-10x, on May 10, 2017 at 7:40 AM

@scott thanks for sharing additional data analysis tools!

Announcements

Let us know what you think about the new 10x Community in the Community Suggestions forum.