List of V(D)J mapping software that works with complex datasets


#1

A list of software that can perform V(D)J mapping for RNA-Seq, single-cell RNA sequencing, etc and extract complex rearrangements typical for lymphomas.

This is a wiki page. Please edit and add software you know about. However, note that this is not the place for closed-source commercial software vendors to advertise their products.

RNA-Seq data:

Single-cell RNA sequencing data:

Complex rearrangements:


B-T.CR Wiki Home
List of downstream analysis software
List of downstream analysis software
#2

Another tool for Single-cell RNA sequencing data

VDJPuzzle:
Eltahla, Auda A; Rizzetto, Simone; Pirozyan, Mehdi R; Betz-Stablein, Brigid D; Venturi, Vanessa; Kedzierska, Katherine; Lloyd, Andrew R; Bull, Rowena A; Luciani, Fabio. “Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells”. Immunology and Cell Biology. doi:10.1038/icb.2016.16


#3

Hi Mikhail,

Can MIGEC be used in TCR sequencing data from single cells?

Cheers


#4

Hello,

The primary goal of MIGEC is to work with UMI(unique molecular identifier)-tagged data. If you have this kind of data is separate files for each of your cells you can process it and then collect it using custom scripts. However, for most single-cell applications I would recommend to use dedicated software tools: VDJpuzzle mentioned above by Simone should work better for you.


#5

Thank you! I have TCR seq data tagged with UMI, from single cells. I’ve been using MiXCR to analyse it but I think it’s not correcting very well the PCR errors. I was wondering if I could use the power of MIGEC to correct PCR errors in the single cell data? Of note, my data it’s not RNA seq data, only TCR seq. Can I use VDJpuzzle anyway?


#6

Depends on your protocol design. You can use MIGEC to de-multiplex samples and assemble UMI-tagged reads into consensus sequences (MIGEC Checkout and Assemble routines, they will generate you FASTQ files with consensus sequences), and perform V-D-J mapping either with MIGEC or any other dedicated software.


#7

That’s great! Thank you so much