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 summary, interrogation, and further processing of IMGT/HighV-QUEST output files. IgAT is a Microsoft Excel based software for the extensive analysis and graphical presentation of very large collections of immunoglobulin (Ig) transcripts which have been pre-analyzed by the web-based IMGT/HighV-QUEST program. It additionally calculates the probability of antigen-driven selection within Ig repertoires and predicts structural properties of the antigen-binding site.
A complementary software suite that solves a wide range of RepSeq post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. The main aims of the VDJtools Project are: (i) Ensure consistency between post-analysis methods and results, (ii) Save the time of bioinformaticians analyzing RepSeq data, (iii) Create an API framework facilitating development of new RepSeq analysis applications, and (iv) Provide a simple enough command line tool so it could be used by immunologists and biologists with little computational background.
Enables users to assign V and J regions of immunoglobulin sequences to their corresponding germline alleles. IgSCUEAL aims to detect recombination breakpoints and affect germline genes from rearranged immunoglobulin genes. This tool utilizes a statistical model of sequence evolution permitting generation of a weighted set of assignments.
Utilizes re-alignment to identify V(D)J genes and alleles after common local alignment. A methodology is developed to correct the PCR and sequencing errors, and to minimize the PCR bias among various rearranged sequences with different V and J gene families. IMonitor provides general adaptation for sequences from all receptor chains of different species and outputs useful statistics and visualizations. Usefulness of IMonitor was demonstrated on minimal residual disease detection of patients with B-cell Acute Lymphoblastic leukemia.
A user-friendly tool for analyzing and visualizing IG and TR repertoires based on NGS data. IMEX offers several algorithms for analyzing the clonality and diversity on multiple levels such as V-(D)-J arrangement, CDR, and nucleotide sequences of the whole reads. Moreover, it also provides features for analyzing primer efficiency. IMEX includes various visualization possibilities such as pie charts, histograms, line charts, bubble charts, and heat maps.