A benchmark of transposon insertion detection tools using real data

Vendrell-Mir, Pol; Barteri, Fabio; Merenciano, Miriam; González, Josefa; Casacuberta, Josep M.; Castanera, Raúl

doi:10.1186/s13100-019-0197-9

Mobile DNA

Table 1 Tools selected for the benchmark of TE insertions

From: A benchmark of transposon insertion detection tools using real data

Tool	Target	Prediction	Input	Output format	Perceived difficulty		Manual
Tool	Target	Prediction	Input	Output format	Installation	Input preparation	Manual
RelocaTE2	Non-reference insertions	All families	fastq	gff file	Easy	Easy	https://github.com/JinfengChen/RelocaTE2
Jitterbug	Non-reference insertions	All families	Bam	gff file	Medium	Medium	https://github.com/elzbth/jitterbug
Retroseq ^a	Non-reference insertions	All families	Bam	vcf file	Easy	Difficult	https://github.com/tk2/RetroSeq/wiki/RetroSeq-Tutorial
ITIS	Non-reference insertions	Single-family	fastq	Bed file	Easy	Medium	https://github.com/Chuan-Jiang/ITIS
MELT	Reference and non-reference insertion	Single-family	Bam	vcf file	Easy	Medium	http://melt.igs.umaryland.edu/manual.php
PopoolationTE2	Reference and non-reference insertions	All families	fastq	Tool-specific	Easy	Easy	https://sourceforge.net/projects/popoolation-te2/
Teflon	Reference and non-reference insertions	All families	fastq	Tool-specific	Medium	Medium	https://github.com/jradrion/TEFLoN
Trackposon	Reference and non-reference insertions	Single-family	fastq	Bed file	Easy	Easy	http://gamay.univ-perp.fr/~Panaudlab/TRACKPOSON.tar.gz
TEMP ^a	Reference and non-reference insertions	All families	Bam	Tool-specific	Easy	Difficult	https://github.com/JialiUMassWengLab/TEMP/blob/master/Manual
TE-locate ^a	Reference and non-reference insertions	All families	Sam	Tool-specific	Easy	Difficult	https://sourceforge.net/projects/te-locate/
PopoolationTE ^a	Reference and non-reference insertions	All families	fastq	Tool-specific	Easy	Difficult	https://sourceforge.net/p/popoolationte/wiki/Workflow/
ngs_te_mapper ^a	Reference and non-reference insertions	All families	fastq	Bed file	Easy	Difficult	https://github.com/bergmanlab/ngs_te_mapper
McClintock	Reference and non-reference insertion	All families	fastq	Bed file	Easy	Difficult	https://github.com/bergmanlab/mcclintock

^a These tools were run as part of the McClintock pipeline. Perceived difficulty refers to McClintock and not the original methods
Installation: Easy = available in Conda, or automatic / semi-automatic installation. Medium = Needs several dependencies or specific versions of packages that need manual installation. Input preparation: Easy = can be run using common formats (ie fasta, bed) without the need of specific formatting. Medium = Needs specific formatting. Difficult = Needs very specific formatting

Back to article page

ISSN: 1759-8753

Contact us

General enquiries: journalsubmissions@springernature.com