Searches and clusters algorithms that can be orders of magnitude. USEARCH is a sequence analysis software which combines different algorithms into a single package. This software searches in database for top global hits and provides several NGS read processing features such as dereplication, paired read overlapping, quality filtering, FASTQ file statistics or chimeric sequence filtering.
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 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.
A little utility to expose the file format conversion in BioPython in a convenient way. Seqmagick can be used to query information about sequence files, convert between types, and modify sequence files. All functions are accessed through subcommands. Most commands support gzip (files ending in .gz) and bzip (files ending in .bz2 or .bz) compressed inputs and outputs.