QtCR : an integrative quality control pipeline for AIRR-sequencing

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Le Gouge, Kenz | Mhanna, Vanessa | Stys, Paul | Coatnoan, Nicolas | Vantomme, Hélène | Barennes, Pierre | Klatzmann, David | Mariotti-Ferrandiz, Encarnita

Edité par CCSD -

International audience. Next-generation sequencing technologies have reshaped the TCR-seq analysis. Increasing sample throughput with dedicated kits and increased depth deeply complexified downstream analysis, often at the cost of a thorough quality control (QC). Indeed, assessing data quality is a crucial step toward subsequent analysis, but it is often overlooked. Skipping this step exposes the researcher to draw conclusions that could be explained by sequencing or data production related issues, costing time and consumables. Here, we propose an integrative QC pipeline for TCR-seq (QtCR), that combines both raw and aligned reads data QC correlated with input biological material with an at-a-glance readout. It provides all the tools to spot inconsistencies between input material and sequenced data, identify outliers and quickly monitor run quality. QtCR pipeline is wrapped in a R shiny-like interface to efficiently skim through all the metrics in an user-friendly interface. QtCR would benefit to all researcher, neophytes or experienced, and aims to fill a need for TCR-centered QC. Tool will be open source and freely available

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