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A computational method to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. TraCeR links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles. TraCeR extracts TCR-derived sequencing reads for each cell by alignment against ‘combinatorial recombinomes’ comprising all possible combinations of V and J segments. Reads are then assembled into contiguous sequences that are analyzed to find full-length, recombined TCR sequences. Importantly, the reconstructed recombinant sequences typically contain nearly the complete length of the TCR V(D)J region and so allow high-confidence discrimination between closely related gene segments. Our method is sensitive, accurate and easy to adapt to any species for which annotated TCR gene sequences are available.
Allows users to reconstruct the native T-cell receptors (TCR)αβ from single cell RNA-seq data of Ag-specific T cells and to link these with the gene expression profile of individual cells. VDJPuzzle enables analysis about TCR diversity and its relationship with the transcriptional profile of different clones. Moreover, single-cell transcriptome analysis can successfully distinguish Ag-specific T cell populations sorted directly from resting memory cells in peripheral blood and sorted after ex vivo stimulation. Moreover, it has been adapted for B-cell receptor (BCRs) and includes additional features to reliably characterizes somatic hypermutation (SHMs).
TRAPeS / TCR Reconstruction Algorithm for Paired-End Single-cell
Reconstructs T cell receptors (TCRs) from paired-end sequencing libraries of single cells, even at short (25 bp) read length. TRAPeS is a software that works on the original reads - leading to increased sensitivity. The TRAPeS algorithm has four main steps: (i) identifying putative pairs of variable (V) and joining (J) segments, (ii) collecting putative CDR3-originating reads, (iii) reconstructing the CDR3 and (iv) separating similar TCRs and determining chain productivity.
BASIC / BCR Assembly from SIngle Cells
Allows investigators to use scRNA-seq for assembling BCR sequences at single cell resolution. BASIC performs semi-de novo assembly in two stages: (i) uses known constant and variable regions to identify anchor sequences, and (ii) uses these anchors to guide the de novo assembly of the BCR. BASIC can help couple gene expression information from scRNA-seq with immune repertoire, and facilitate studies between B-cell receptor features, clonality, differentiation and transcriptional programming at single cell resolution.
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