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Table 1 Tools selected for the benchmark of TE insertions

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

ToolTargetPredictionInputOutput formatPerceived difficultyManual
InstallationInput preparation
RelocaTE2Non-reference insertionsAll familiesfastqgff fileEasyEasyhttps://github.com/JinfengChen/RelocaTE2
JitterbugNon-reference insertionsAll familiesBamgff fileMediumMediumhttps://github.com/elzbth/jitterbug
Retroseq aNon-reference insertionsAll familiesBamvcf fileEasyDifficulthttps://github.com/tk2/RetroSeq/wiki/RetroSeq-Tutorial
ITISNon-reference insertionsSingle-familyfastqBed fileEasyMediumhttps://github.com/Chuan-Jiang/ITIS
MELTReference and non-reference insertionSingle-familyBamvcf fileEasyMediumhttp://melt.igs.umaryland.edu/manual.php
PopoolationTE2Reference and non-reference insertionsAll familiesfastqTool-specificEasyEasyhttps://sourceforge.net/projects/popoolation-te2/
TeflonReference and non-reference insertionsAll familiesfastqTool-specificMediumMediumhttps://github.com/jradrion/TEFLoN
TrackposonReference and non-reference insertionsSingle-familyfastqBed fileEasyEasyhttp://gamay.univ-perp.fr/~Panaudlab/TRACKPOSON.tar.gz
TEMP aReference and non-reference insertionsAll familiesBamTool-specificEasyDifficulthttps://github.com/JialiUMassWengLab/TEMP/blob/master/Manual
TE-locate aReference and non-reference insertionsAll familiesSamTool-specificEasyDifficulthttps://sourceforge.net/projects/te-locate/
PopoolationTE aReference and non-reference insertionsAll familiesfastqTool-specificEasyDifficulthttps://sourceforge.net/p/popoolationte/wiki/Workflow/
ngs_te_mapper aReference and non-reference insertionsAll familiesfastqBed fileEasyDifficulthttps://github.com/bergmanlab/ngs_te_mapper
McClintockReference and non-reference insertionAll familiesfastqBed fileEasyDifficulthttps://github.com/bergmanlab/mcclintock
  1. a These tools were run as part of the McClintock pipeline. Perceived difficulty refers to McClintock and not the original methods
  2. 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