TSSV specifications


Unique identifier OMICS_13758
Alternative name Targeted characterisation of Short Structural Variation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequencing data, a library containing a list of loci of interest
Input format FASTA
Output data An overview of marker pair alignments, a detailed description of the identified alleles, their respective frequency per strand, supporting reads of each locus of interest in separate FASTA files
Output format FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License MIT License
Computer skills Advanced
Version 0.4.2
Stability Beta
Source code URL https://git.lumc.nl/j.f.j.laros/tssv/
Maintained Yes




No version available


  • person_outline Seyed Yahya Anvar

Publication for Targeted characterisation of Short Structural Variation

TSSV citation


Analysis of amplicon based NGS data from neurological disease gene panels: a new method for allele drop out management

BMC Bioinformatics
PMCID: 5123238
PMID: 28185542
DOI: 10.1186/s12859-016-1189-0

[…] con as a putative allele or an artifact []. Advances in the bioinformatics field led to the creation and the development of algorithms to manage such artifacts during the analysis (e.g.: AmpliVar [], TSSV [] and Mutascope []). AmpliVar is based on the reduction of the number of input reads to be aligned to a reference genome by grouping for primer sequence in a key-value structure, where each grou […]

TSSV institution(s)
Department of Human Genetic, Leiden University Medical Center, Leiden, Netherlands; Leiden Genome Technology Center, Leiden University Medical Center, Leiden, Netherlands; Netherlands Bioinformatics Centre, Leiden, Netherlands
TSSV funding source(s)
This work was partially supported by the Centre for Molecular Systems Biology (CMSB), Duchenne Parent Project (the Netherlands) and a grant from the Netherlands Genomics Initiative (NGI)/Netherlands Organization for Scientific Research (NWO) within the framework of the Forensic Genomics Consortium Netherlands.

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