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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 fileEasyEasy
JitterbugNon-reference insertionsAll familiesBamgff fileMediumMedium
Retroseq aNon-reference insertionsAll familiesBamvcf fileEasyDifficult
ITISNon-reference insertionsSingle-familyfastqBed fileEasyMedium
MELTReference and non-reference insertionSingle-familyBamvcf fileEasyMedium
PopoolationTE2Reference and non-reference insertionsAll familiesfastqTool-specificEasyEasy
TeflonReference and non-reference insertionsAll familiesfastqTool-specificMediumMedium
TrackposonReference and non-reference insertionsSingle-familyfastqBed fileEasyEasy
TEMP aReference and non-reference insertionsAll familiesBamTool-specificEasyDifficult
TE-locate aReference and non-reference insertionsAll familiesSamTool-specificEasyDifficult
PopoolationTE aReference and non-reference insertionsAll familiesfastqTool-specificEasyDifficult
ngs_te_mapper aReference and non-reference insertionsAll familiesfastqBed fileEasyDifficult
McClintockReference and non-reference insertionAll familiesfastqBed fileEasyDifficult
  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