A universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments.
Allows users to analyze T-cell antigen receptor (TCR) sequencing data. MiTCR is a program permitting the study of hundreds of millions of raw high-throughput sequencing reads containing sequences encoding human or mouse a or TCR chains. It also allows the extraction of -cell clones from next generation sequencing (NGS) data.
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.
A computational framework for Bayesian estimation of antigen-driven selection in immunoglobulin sequences based on the analysis of somatic mutation patterns. BASELINe represents a fundamental advance over previous methods by shifting the problem from one of simply detecting selection to one of quantifying selection. Along with providing a more intuitive means to assess and visualize selection, BASELINe allows comparative analysis between groups of sequences derived from different germline V(D)J segments.
Identifies novel immunoglobulin (Ig) variable (V) segment alleles based on the analysis of mutation patterns in Rep-Seq data. TIgGER is an automated method that infers the genotype of a subject and corrects the initial allele assignments. It detects novel alleles by analyzing the apparent mutation frequency pattern at each nucleotide position as a function of the sequence-wide mutation count.
Provides an Hidden Markov Model (HMM)-based framework for studying B-cell receptor sequence (BCRs). Partis is an open source software able to annotate, simulate, and infer clonal family of BCRs. The program deduces parameters about the rearrangement process before performing annotation inference on each sequence in the set. It intends to be effective for analyzing modern large sequencing data sets.
Allows users to analyze T-cell receptor (TCR) repertoire sequences produced by deep sequencing. Decombinator is a program that employs a string matching algorithm to search the FASTQ files produced by high-throughput sequencing (HTS) machines for rearranged TCR sequence. This pipeline contains a central algorithm searches for 'tag' sequences, the presence of which indicates the inclusion of particular V or J genes in a recombination.
Identifies germline V genes from expressed repertoires to a specificity of 100%. IgDiscover uses a cluster identification process to produce candidate sequences that, once filtered, results in individualized germline V gene databases. IgDiscover was tested in multiple species, validated by genomic cloning and cross library comparisons and produces comprehensive gene databases even where limited genomic sequence is available. IgDiscover analysis of the allelic content of the Indian and Chinese-origin rhesus macaques reveals high levels of immunoglobulin gene diversity in this species.
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).
A software package that significantly improves the completeness and accuracy of TCR/IG profiling from deep sequence data and includes procedures to identify novel alleles of gene segments. The alignment step in LymAnalyzer, which is based on a fast-tag-searching algorithm, results in rapid identification of VDJ gene segments, with significantly improved accuracy and completeness compared to existing tools applied to TCR data. In addition, LymAnalyzer can be applied to IG sequences, includes an integrated single nucleotide polymorphism (SNP) calling algorithm that identifies novel alleles of the VDJ gene segments and produces lineage mutation trees to represent the affinity maturation process of the IGs. On real and simulated data sets LymAnalyzer produces highly accurate and complete results. Although, to date we have applied it to TCR/IG data from human and mouse, it can be applied to data from any species for which an appropriate database of reference genes is available.
Handles alignments with insertions/deletions (indels), while maintaining or improving the speed. HTJOINSOLVER is a desktop application, provided as an implementation of the partitioning method. Similar to the original JOINSOLVER algorithm, it conserves motifs to initiate the alignment process. The original algorithm was developed as a fast and accurate method, but was not designed to handle indels.
Assists users in automating analysis of the generated next-generation-sequencing-spectratyping (NGS-S) data. TCRProfiler is a software that allows users (i) to determine, for each T cell receptor beta locus (TRB) chain analyzed, the exact length and sequence of the CDR3, (ii) to identify the rearranged TRBV (variable), TRBD (diversity) and TRBJ (joining) genes, (iii) to analyze nontemplate nucleotides added at the junction sites, and (iv) to exclude non-functional transcripts.
Provides a suite of utilities that cover a range of complex analysis tasks for immunoglobulin (Ig) repertoire sequencing data. Change-O is a suite of utilities that (i) processes the output of V(D)J alignment tools, (ii) assigns clonal clusters to Ig sequences and (iii) reconstructs germline sequences. It also offers applications to import data from the frequently used IMGT/HighV-QUEST tool and a set of utilities to perform basic database operations, such as sorting, filtering and modifying annotations.
Analyzes vast amounts of IGHV (immunoglobulin heavy-chain variable) sequences and exploring the resulting data. ImmuneDB can take as input raw FASTA/FASTQ data, identify genes, determine clones, construct lineages, as well as provide information such as selection pressure and mutation analysis. It uses an industry leading database, MySQL, to provide fast analysis and avoid the complexities of using error prone flat-files. After analysis, resulting data can then be easily visualized, queried, and exported through its web-based interface.
A method to derive clonotype repertoires from next generation sequencing data with sophisticated routines for handling errors stemming from PCR and sequencing artefacts. The application can handle different kinds of input data originating from single- or paired-end sequencing in different configurations and is generic regarding the species and gene of interest.
Performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires. IgRepertoireConstructor takes Illumina MiSeq paired end reads as an input and expect that each left and right reads overlap and cover variable region of antibody. IgRepertoireConstructor stitches paired-end reads and removes contaminations using alignment of stitched reads against Ig germline database. This procedure significantly improves quality of input reads and allows one to constructs reads covering variable region of antibody.