Table 1 Software for detecting transposable element insertions from WGS data

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/