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Table 1 Software for detecting transposable element insertions from WGS data

From: Transposable element detection from whole genome sequence data

Name of method Detection target Ref. Notes or use case Implementation Availability
TranspoSeq Transposable elements [40] Analysis of Tumour/Normal WGS pairs, extension to analyse WES data as well Java, R https://www.broadinstitute.org/cancer/cga/transposeq
Tea Transposable elements [65] Analysis of Tumour/Normal WGS Pairs R http://compbio.med.harvard.edu/Tea/
TraFiC Transposable elements [66] Analysis of Tumour/Normal WGS Pairs, detection of transduced sequences Perl https://github.com/cancerit/TraFiC
RetroSeq Transposable elements [50, 51] Used for analysis of mouse strain genomes, also demonstrated on human, has genotyping and discovery modes Perl https://github.com/tk2/RetroSeq
Tangram Transposable elements [75] Demonstrated on 1000 Genomes Project samples, includes genotyping capability C, C++ https://github.com/jiantao/Tangram
VariationHunter Structural Variants [76, 77] Among the first methods to detect polymorphic Alu insertions from WGS C++ http://compbio.cs.sfu.ca/software-variation-hunter
GRIPper Retrotransposed mRNAs [78] Used to detect non-reference gene retrocopy insertions. Demonstrated in humans, mice, and chimpanzees. Python https://github.com/adamewing/GRIPper
T-lex/T-lex2 Transposable elements [52, 53] Detects both insertions versus the reference and absences of reference elements in other genomes. Demonstrated on Drosophila TEs. Perl http://petrov.stanford.edu/cgi-bin/Tlex.html
HYDRA-SV Structural rearrangements [79] General-purpose SV detection, also detects TE insertions C++, Python https://github.com/arq5x/Hydra
RelocaTE Transposable elements [80] Demonstrated on mPing insertions in Oryza sativa (rice) Perl https://github.com/srobb1/RelocaTE
ITIS Transposable elements [81] Used to detect Tnt1 insertions in Medicago truncatula Perl http://bioinformatics.psc.ac.cn/software/ITIS/
ngs_te_mapper Transposable elements [82] Requires TSDs, demonstrated in Drosophila R https://github.com/bergmanlab/ngs_te_mapper
TE-Locate Transposable elements [83] Used to examine TE insertions in Arabidopsis populations Java, Perl http://sourceforge.net/projects/te-locate/
TIGRA Structural rearrangements [84] Assembly-based SV detection method, demonstrated to identify TE breakpoints C++ https://bitbucket.org/xianfan/tigra
Mobster Transposable elements [85] Demonstrated on WGS and WES data, Illumina and ABI SOLiD data. Java http://sourceforge.net/projects/mobster/
TEMP Transposable elements [86] Geared towards population-level TE detection from pooled data Perl https://github.com/JialiUMassWengLab/TEMP
TE-Tracker Transposable elements [87] Attempts to determine source elements in reference. Demonstrated on Arabidopsis. Perl http://www.genoscope.cns.fr/externe/tetracker/
Jitterbug Transposable elements [41] Demonstrated on Human and Arabidopsis. Python http://sourceforge.net/projects/jitterbug/
DD_DETECTION Transposable elements [88] Does not require input of canonical TE sequences (Database-free) C++ https://bitbucket.org/mkroon/dd_detection
MELT Transposable elements [89] Used for comprehensive analysis of 2504 participants in the 1000 Genomes Project Java http://melt.igs.umaryland.edu/