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