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.
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 analysis of the complete immune repertoire of different species. ARGalaxy is a web server for analyzes and visualization of T-cell receptor (TCR) and B-Cell Receptor (BCR) sequencing data. It consists of four parts: the demultiplex tool, the international ImMunoGeneTics information system (IMGT) concatenate tool, the immune repertoire pipeline, and the somatic hypermutation (SHM) and class switch recombination (CSR) pipeline. All parts can be run independently or combined, depending on the available data and the question of interest.
Assists users to estimate the diversity of an organism’s B- and T-cell repertoires. Recon consists of a modified maximum-likelihood method that outputs the overall diversity of a repertoire from measurements on a sample. This program is able to perform estimations by any of a vast set of complementary diversity measures, including species richness and entropy, at fractional repertoire coverage.
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.
Provides methods to investigate lymphocyte receptor clonal lineages, diversity, gene usage, and other repertoire level properties. Alakazam was developed to (i) provides core functionality for R packages in the Immcantation framework, (ii) provides an R interface for interacting with the output of the pRESTO and Change-O tool suites, (iii) performs lineage reconstruction on clonal populations of immunoglobulin (Ig) sequences and analyzing the topology of the resultant lineage trees, (iv) performs clonal abundance and diversity analysis on lymphocyte repertoires and, (v) performs physicochemical property analyses of lymphocyte receptor sequences.