ArticleG3 (Bethesda, Md.)2017
McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data.
Article in G3 (Bethesda, Md.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed, 93 citations in OpenAlex.
- Ancient Transposable Elements Sustain Global Ecological Adaptation Despite Chronically Low Nucleotide Diversity.Molecular ecology · 2026Article
- Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping.Genetics · 2026Article
- Meiotic double-strand DNA breaks and spontaneous mutation in Drosophila melanogaster.G3 (Bethesda, Md.) · 2026Article
- MycoMobilome: a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom.NAR genomics and bioinformatics · 2026Article
- Massive proliferation of retrotransposons contributes to genome size expansion in species of the Pseudocercospora genus.Mobile DNA · 2026Article
- The contribution of transposable element insertions to genetic diversity inbioRxiv : the preprint server for biology · 2025Article
- Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies.Plant biotechnology journal · 2025Article
- Experimental evolution of Saccharomyces cerevisiae for caffeine tolerance alters multidrug resistance and target of rapamycin signaling pathways.G3 (Bethesda, Md.) · 2024Article
- Harbinger transposon insertion in ethylene signaling gene leads to emergence of new sexual forms in cucurbits.Nature communications · 2024Article
- Experimental evolution ofbioRxiv : the preprint server for biology · 2024Article
- Study of Dispersed Repeats in theInternational journal of molecular sciences · 2024Article
- Article
- Mobile element insertions in rare diseases: a comparative benchmark and reanalysis of 60,000 exome samples.European journal of human genetics : EJHG · 2024Article
- Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.Mobile DNA · 2023Article
- Article
- TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.Genome biology · 2023Article
- Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.bioRxiv : the preprint server for biology · 2023Article
- Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium.Genetics · 2023Article
- Caffeine-tolerant mutations selected through an at-home yeast experimental evolution teaching lab.bioRxiv : the preprint server for biology · 2023Article
- Caffeine-tolerant mutations selected through an at-home yeast experimental evolution teaching lab.microPublication biology · 2023Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Transposable element (TE) insertions are among the most challenging types of variants to detect in genomic data because of their repetitive nature and complex mechanisms of replication . Nevertheless, the recent availability of large resequencing data sets has spurred the development of many new methods to detect TE insertions in whole-genome shotgun sequences. Here we report an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods. We demonstrate the utility of McClintock by evaluating six TE detection methods using simulated and real genome data from the model microbial eukaryote,
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.