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IMSEQ specifications


Unique identifier OMICS_08586
Alternative name IMmunogenetic SEQuence Analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequencing data
Input format FASTA, FASTQ
Operating system Unix/Linux, Mac OS
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.1
Stability Stable
Maintained Yes


No version available


  • person_outline Leon Kuchenbecker

Publication for IMmunogenetic SEQuence Analysis

IMSEQ citations


Overview of methodologies for T cell receptor repertoire analysis

BMC Biotechnol
PMCID: 5504616
PMID: 28693542
DOI: 10.1186/s12896-017-0379-9

[…] Over the past years different tools and strategies have been developed for immune repertoire analysis, of which some have been summarized in previous reviews [, , –]. Other methods, such as IMSEQ [], TCRklass, iMonitor [], LymAnalyzer [] and RTRC [], have however emerged since. A popular tool is MiXCR (previously MiTCR), developed by Bolotin et al. [], which allows for a highly customiza […]


BRILIA: Integrated Tool for High Throughput Annotation and Lineage Tree Assembly of B Cell Repertoires

Front Immunol
PMCID: 5239784
PMID: 28144239
DOI: 10.3389/fimmu.2016.00681

[…] ] to fine-tune the annotations (). Examples of other algorithms that use similar alignment-based annotation methods include IgBlast (), SoDA (), JointML (), JOINSOLVER (), VDJSeq-Solver (), MiXCR (), IMSEQ (), and IgSQUEAL (). A different strategy, hidden Markov modeling (HMM), uses statistical models and probability matrices to calculate the most likely series of events leading to each sequence. […]


Vidjil: A Web Platform for Analysis of High Throughput Repertoire Sequencing

PLoS One
PMCID: 5106020
PMID: 27835690
DOI: 10.1371/journal.pone.0166126

[…] V(D)J recombinations were developed by IMGT [, ]. Recently, new software able to deal with up to millions of sequences have appeared: [], IgBlast [], Decombinator [], miTCR [], TCRKlass [], MiXCR [], IMSEQ []. At the heart of these programs is optimized comparison of the reads against germline databases to detect and quantify clonotypes, whose definitions are supposed to overlap as much as possibl […]


Immune DNA signature of T cell infiltration in breast tumor exomes

Sci Rep
PMCID: 4958917
PMID: 27452728
DOI: 10.1038/srep30064

[…] e human TCRB region (hg19: chr7:142,000,817–142,510,993) and the unmapped reads were extracted from the BAM files, and converted to fastq using SAMtools and BEDtools. The tools ClonotypeR, MiTCR, and IMSEQ were used to identify rearranged TCR regions from the resulting files. Human TCR references were provided by MiTCR and IMSEQ. We created our own reference for ClonotypeR as specified in the docu […]


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IMSEQ institution(s)
Charité Universitätsmedizin Berlin, Berlin, Germany

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