SatTCR pipeline

SatTCR is a Snakemake pipeline for assembling T Cell Receptor (TCR) repertoire data by using MIXCR, and perform a saturation analysis.

TCR profiling

Profiling the TCR repertoire using next-generation sequencing (NGS) to quantify adaptive immune responses has become common in human and animal research. TCR counts from NGS data provide a way to quantify T cell response to vaccines, cancer, or infectious diseases for preclinical and clinical health studies.

SatTCR modules

SatTCR is composed by 4 modules described in the image below:

• Quality control: QC diagnostics of the sequencing data.

• Clonotype assembly: Assembly of the TCR clonotypes using MIXCR

• Saturation analysis:: Sequential bootstrapping of the sequencing data to assembly clonotypes with a fixed # of sequencing reads.

• Report of SatTCR results: The report contains data visualization of statistics summarizing the TCR repertoire assembled with the complete data and sampled version of the sequencing files.

How interpret SatTCR results?

A SatTCR provides multiple analysis. The key points to pay attention are:

References

• Bolotin DA, Poslavsky S, Mitrophanov I, Shugay M, Mamedov IZ, Putintseva EV, Chudakov DM. _“MiXCR: software for comprehensive adaptive immunity profiling_”. Nature methods (2015)

• Bolotin DA, Poslavsky S, Davydov AN, Frenkel FE, Fanchi L, Zolotareva OI, Hemmers S, Putintseva EV, Obraztsova AS, Shugay M, Ataullakhanov RI, Rudensky AY, Schumacher TN, Chudakov DM. “Antigen receptor repertoire profiling from RNA-seq data”. Nature Biotechnology 35, (2017)

• Greiff V, Miho E, Menzel U, Reddy ST. “Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires”. Trend in Immunology (2015)