A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information). The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs. Example of such mapping programs are: Blat, SHRiMP, LastZ, MAQ and many many others.
Searches for germline variable (V), diversity (D) and joining (J) genes matches for T-cell receptor (TCR) and immunoglobulin (IG) sequences using BLAST algorithm. Works both with amino-acid and nucleotide sequences and supports alignment to IMGT(R) germline sequence database, as well as custom databases. Provides information of CDR1,2 and FR1,2,3 region markup and germline sequence mutations.
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.
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.