IMSEQ is a fast, PCR and sequencing error aware tool to analyze high throughput data from recombined T-cell receptor or immunoglobolin gene sequencing experiments. It derives immune repertoires from sequencing data in FASTA / FASTQ format.

IMSEQ Workflow

Please cite the following publication when you use IMSEQ:

Kuchenbecker L, Nienen M, Hecht J, Neumann AU, Babel N, Reinert K, Robinson PN. IMSEQ - a fast and error aware approach to immunogenetic sequence analysis. Bioinformatics. 2015;31(18):2963–71. [PubMed] [Journal] [BibTeX]

Getting IMSEQ

IMSEQ is freely available and its source code is made available under the GPLv2 license. You can obtain binaries and sources for the latest release, IMSEQ 1.1.0, by choosing from one of the following links:

Changes can be reviewed in the Changelog.

For the sources and build instructions of the current development version check out the GitHub repository.


IMSEQ requires at least two input files and the specification of at least one output file. The two input files are specified using the switches

$ imseq -ref segment-reference.fa -o output-file.tsv input-file.fastq.gz

Further Reading

IMSEQ supports many more options that can adjust its behaviour to many experimental conditions. All options are documented in the Manual. Furthermore, the Tutorial will guide you through some basic analysis of the example files that come with IMSEQ.