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.
Involves data processing, clustering, assembly, and optimization. IMPre is a method that provides a comprehensive approach for identification of novel B- and T-cell receptor (BCR/TCR) genes and alleles in certain species with greatly improved speed, cost, and accuracy. This de novo package comprises four main steps: data processing, clustering, assembly, and optimization. IMPre is stable with animal and long-sequence data.
A stand-alone pipeline primarily based in R programming for the integral analysis of B cell repertoire data generated by HTS. The pipeline integrates GNU software and in house scripts to perform quality filtering, sequencing noise correction and repertoire reconstruction based on V, D and J segment assignment, clonal origin and unique heavy chain identification. Post-analysis scripts generate a wealth of repertoire metrics that in conjunction with a rich graphical output facilitates sample comparison and repertoire mining. The performance of ImmunediveRsity was tested with raw and curated human and mouse 454-Roche sequencing benchmarks providing good approximations of repertoire structure. Although ImmunediveRsity is similar to other recently developed tools, it offers significant advantages that facilitate repertoire analysis and repertoire mining. ImmunediveRsity is open source and free for academic purposes and it runs on 64 bit GNU/Linux and MacOS.
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.
Annotates next-generation sequencing data, identifies transcripts in a lineage of interest, and tracks lineage development across multiple time points. SONAR is capable of automating both general repertoire analysis and specialized techniques for investigating specific lineages. It also generates figures, such as identity–divergence plots and longitudinal phylogenetic “birthday” trees, and provides interfaces to other programs such as DNAML and BEAST. This software provides a tool for the processing of large next-generation sequencing datasets and the ontogenic analysis of neutralizing antibody lineages.