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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
Tea Transposable elements [65] Analysis of Tumour/Normal WGS Pairs R
TraFiC Transposable elements [66] Analysis of Tumour/Normal WGS Pairs, detection of transduced sequences Perl
RetroSeq Transposable elements [50, 51] Used for analysis of mouse strain genomes, also demonstrated on human, has genotyping and discovery modes Perl
Tangram Transposable elements [75] Demonstrated on 1000 Genomes Project samples, includes genotyping capability C, C++
VariationHunter Structural Variants [76, 77] Among the first methods to detect polymorphic Alu insertions from WGS C++
GRIPper Retrotransposed mRNAs [78] Used to detect non-reference gene retrocopy insertions. Demonstrated in humans, mice, and chimpanzees. Python
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
HYDRA-SV Structural rearrangements [79] General-purpose SV detection, also detects TE insertions C++, Python
RelocaTE Transposable elements [80] Demonstrated on mPing insertions in Oryza sativa (rice) Perl
ITIS Transposable elements [81] Used to detect Tnt1 insertions in Medicago truncatula Perl
ngs_te_mapper Transposable elements [82] Requires TSDs, demonstrated in Drosophila R
TE-Locate Transposable elements [83] Used to examine TE insertions in Arabidopsis populations Java, Perl
TIGRA Structural rearrangements [84] Assembly-based SV detection method, demonstrated to identify TE breakpoints C++
Mobster Transposable elements [85] Demonstrated on WGS and WES data, Illumina and ABI SOLiD data. Java
TEMP Transposable elements [86] Geared towards population-level TE detection from pooled data Perl
TE-Tracker Transposable elements [87] Attempts to determine source elements in reference. Demonstrated on Arabidopsis. Perl
Jitterbug Transposable elements [41] Demonstrated on Human and Arabidopsis. Python
DD_DETECTION Transposable elements [88] Does not require input of canonical TE sequences (Database-free) C++
MELT Transposable elements [89] Used for comprehensive analysis of 2504 participants in the 1000 Genomes Project Java