Is There Any Tool For High Throughput Immunoglobulin Repertoire Sequencing Data Analysis?

Question

[yuyaxuan0]

Hi,

I know there are tools like MitCR and Decombinator for TCR sequencing analysis. But for Immunoglobulins sequences, so far I only know that IgBlast and IMGT/IGV can assign V/D/J segments and finding the CDR3 for the inputed sequence.

If there are no tools for this, do you think it would be a good idea to develop one for that? I am kind of interested in making one.

Answer 1

[mikhail.shugay]

Hello,

Hmm just noticed this question via "similar posts". If you need to analyze Ig data I can suggest two tools based on what data do you have

1. If you don't have full-length sequences or you could omit Variable segment hypermutations and focus on CDR3 you can use CdrBlast tool from MiGEC pipeline
2. If you have full-length sequences (454 or MiSeq 300+300bp reads) you can use IgBlastWrapper available here. It offers two important features: a) parallel FASTQ processing, tabular output and implicit clonotype assembly b) It actually performs CDR3 extraction, while there is no way to directly obtain CDR3 sequences from vanilla standalone IgBlast