May 25, 2017

The Chromium Single Cell V(D)J Software Suite is here!

Shauna Clark

The new Chromium™ Single Cell V(D)J Software Suite is a complete package for assembling, visualizing and analyzing V(D)J sequences and clonotypes from single cell data produced using the Chromium™ Single Cell V(D)J Solution.  The suite includes:

Cell Ranger 2.0 - the only commercially available tool for discovery and evaluation of full-length paired T-cell receptor alpha and beta transcripts, quantifies those V(D)J transcripts at the single cell level

Loupe V(D)J Browser - a desktop application that allows you to analyze, search, and visualize V(D)J sequences and clonotypes from single cell data

What’s new with Cell Ranger 2.0?

  • A new set of analysis pipelines that provides de novo assembled, paired T-cell receptor sequences spanning from the 5' end through the V(D)J gene segments to the constant region.
  • Returns V(D)J sequences in standard FASTA and FASTQ formats with per-base assembly quality scores
  • Fully annotates and quantifies observed V(D)J transcripts including CDR3 sequence and translation
  • Groups cells by paired sequence into clonotypes for downstream analysis
  • Features both V(D)J sequence assembly and paired clonotype calling
  • Improves runtime performance and bug fixes for Single Cell 3' Gene Expression

What can you do with Loupe V(D)J Browser 1.0?

  • Easily and interactively explore V(D)J data from Cell Ranger 2.0
  • Display counts of paired V(D)J transcripts and clonotypes
  • Visually detect variants and explores sequences down to the read level on a single-cell basis
  • Export charts and copy sequences into your preferred analysis tools
  • Search for CDR3 motifs within T-cell receptor chains

Download software

Additional Resources

Get started with the Loupe V(D)J Browser tutorial

Download V(D)J T cell datasets

Cell Ranger 2.0 Gene Expression release notes