McClintock specifications


Unique identifier OMICS_14560
Name McClintock
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A reference genome, a consensus set of TE sequences and a paired end sequencing read.
Input format FASTA, FASTQC
Output format BED
Operating system Unix/Linux, Mac OS
Programming languages Java, Perl
Computer skills Advanced
Stability Stable
FASTQC, RepeatMasker, R, BWA, BioPerl, SAMtools, Blat, Bowtie, BEDTools, twoBitToFa, BCFTools, Exonerate
Maintained Yes




No version available



  • person_outline Casey Bergman

Publication for McClintock

McClintock citations


The case for not masking away repetitive DNA

PMCID: 5930866
PMID: 29743957
DOI: 10.1186/s13100-018-0120-9

[…] sis, even though read mapping technologies have evolved or have been specifically designed to efficiently assay repetitive DNA from whole genome data. These tools include MELT, RetroSeq, EpiTEome and McClintock for TE insertion site identification [–], T-lex to identify presence/absence of TE copies [], Clari-TE to resolve nested TE structure [], TEtoolkit/TEtranscripts for TE enrichment analysis […]


Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low Coverage Genomes

Genome Biol Evol
PMCID: 5737362
PMID: 28985298
DOI: 10.1093/gbe/evx170

[…] ptember 2017. Easy configuration and the modular architecture make it convenient to adapt TeddyPi to process data from a broad range of TE/SV callers or other integration pipelines such as SVMerge or McClintock (; ). TeddyPi can be applied to any group of organisms where accurate TE/SV calling is feasible. […]

McClintock institution(s)
Faculty of Life Sciences, University of Manchester, Manchester, UK; Centro de Biotecnologia e Química Fina (CBQF), Universidade Católica Portuguesa, Porto, PT; Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA, USA
McClintock funding source(s)
This work was supported by Wellcome Trust Award 096602/B/11/Z.

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