Glossary

  • Adaptive error correction

    “Adaptive error correction” is a method developed by the ENPICOM team, with the aim to correct for sequencing errors in repertoire sequencing data. In short, the error rate of an individual sequencing run is estimated and associated with the quality scores provided by the sequencing machine. This information is subsequently used by a statistical model to determine whether specific sequences is erroneous and whether these errors can be corrected using information from highly similar sequences.

  • Clone Browser

    The Clone Browser is a component of the IGX Platform that is designed specifically for the management of repertoire sequencing data. It contains all clone collections currently loaded onto the platform and serves as an interface for the applications in the platform. 

  • Flexible at the front

    IGX currently supports Illumina FASTQ data fromBCR (heavy, lambda, and kappa chains) and TCR (alpha and beta chains) sequencing experiments from both DNA and RNA of human and murine samples.

  • Generation probability

    The generation probability of a sequence is the probability of observing a specific sequence barring any selection pressures on the immune cells in which these sequences are encoded. This is calculated by merging the probabilities of all recombination events (and non-templated indels) that could potentially lead to the formation of the sequence in question.

  • IGX App

    IGX Apps are separate units inside the IGX Platform with specific analysis capabilities.

    IGX-Explore

    IGX-Explore is an app inside the IGX Platform that features explorative downstream analyses.

    Immune Repertoire

    An Immune Repertoire refers to a collection of B or T cell receptors. Often, this collection is a sample or a cell. 

    Immunomics

    Immunomics is the study of the immune system using omics techniques (e.g. genomics, proteomics, transcriptomics). 

    IGX-Profile 

    IGX-Profile is an app inside the IGX Platform that performs clone identification and quantification.

  • Phylogenetic tree

    Sometimes also referred to as a “clonal lineage”. Each tree represents a lineage that arises from an independent VDJ recombination event. This tree is generally rooted at the inferred sequence that should have resulted from genomic recombination. All other nodes in the tree represent unique (observed or inferred) sequences, that generally differ from the root due to somatic hypermutation or uncorrected sequencing errors.

  • UMI

    Unique molecular identifiers (UMIs) are short sequences or molecular “tags” that can be added during library preparation to mark individual molecules and help to control for PCR errors.

  • Workflow

    A workflow is a sequence of operations that is often repeatedly executed. In the IGX Platform specifically, it is referred to as a sequence of actions (steps performed by the user) in the platform. 

Single-cell and beyond: How to better exploit paired-chain immune repertoire data ON-DEMAND WEBINAR

How can you make the most out of your single-cell Rep-Seq data? Watch our on-demand webinar and learn how to leverage your paired-chain immune repertoire data to advance your research.