Logo do repositório
 
Publicação

McClintock: an integrated pipeline for detecting transposable element insertions in whole-genome shotgun sequencing data

2017Artigo científico Acesso aberto
Ver registo simples
dc.contributor.authorNelson, Michael G.
dc.contributor.authorLinheiro, Raquel S.
dc.contributor.authorBergman, Casey M.
dc.date.accessioned2018-11-08T11:07:08Z
dc.date.available2018-11-08T11:07:08Z
dc.date.issued2017
dc.description.abstractTransposable 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, Saccharomyces cerevisiae. We find substantial variation among McClintock component methods in their ability to detect nonreference TEs in the yeast genome, but show that nonreference TEs at nearly all biologically realistic locations can be detected in simulated data by combining multiple methods that use split-read and read-pair evidence. In general, our results reveal that split-read methods detect fewer nonreference TE insertions than read-pair methods, but generally have much higher positional accuracy. Analysis of a large sample of real yeast genomes reveals that most McClintock component methods can recover known aspects of TE biology in yeast such as the transpositional activity status of families, target preferences, and target site duplication structure, albeit with varying levels of accuracy. Our work provides a general framework for integrating and analyzing results from multiple TE detection methods, as well as useful guidance for researchers studying TEs in yeast resequencing data.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationNelson, M.G., Linheiro, R.S., Bergman, C.M. (2017). McClintock: An integrated pipeline for detecting transposable element insertions in whole-genome shotgun sequencing data. G3: Genes, Genomes, Genetics, 7(8), 2763-2778pt_PT
dc.identifier.doi10.1534/g3.117.043893pt_PT
dc.identifier.eid85027252907
dc.identifier.issn2160-1836
dc.identifier.pmid28637810
dc.identifier.urihttp://hdl.handle.net/10400.14/26009
dc.identifier.wos000407314000031
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherGenetics Society of Americapt_PT
dc.relation096602/B/11/Z
dc.relationRGY0093/2012
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectTransposable elementspt_PT
dc.subjectBioinformaticspt_PT
dc.subjectGenomicspt_PT
dc.subjectYeastpt_PT
dc.titleMcClintock: an integrated pipeline for detecting transposable element insertions in whole-genome shotgun sequencing datapt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.endPage2778
oaire.citation.issue8
oaire.citation.startPage2763
oaire.citation.titleG3: Genes, Genomes, Geneticspt_PT
oaire.citation.volume7
person.familyNameLinheiro
person.familyNameBergman
person.givenNameRaquel
person.givenNameCasey
person.identifier.orcid0000-0003-2659-0910
person.identifier.orcid0000-0002-5462-9854
person.identifier.ridF-7854-2010
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
relation.isAuthorOfPublication9b28d209-23fb-47eb-b105-7cf1fce6c6fa
relation.isAuthorOfPublication3d6ea432-999f-4d17-ada1-0e48359b1671
relation.isAuthorOfPublication.latestForDiscovery9b28d209-23fb-47eb-b105-7cf1fce6c6fa

Ficheiros

Principais
A mostrar 1 - 1 de 1
Miniatura indisponível
Nome:
26762032.pdf
Tamanho:
2.14 MB
Formato:
Adobe Portable Document Format
Ver/Abrir
Licença
A mostrar 1 - 1 de 1
Miniatura indisponível
Nome:
license.txt
Tamanho:
3.44 KB
Formato:
Item-specific license agreed upon to submission
Descrição:
Ver/Abrir

Coleções

CBQF - Contribuições em Revistas Científicas / Contribution to Journals