T-lex3 : An accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data
Bogaerts-Márquez, María (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Barrón Aduriz, Maite Garazi (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Fiston-Lavier, Anna-Sophie (Institut des Sciences de l'Evolution de Montpellier)
Vendrell Mir, Pol (Centre de Recerca en Agrigenòmica)
Castanera, Raúl (Centre de Recerca en Agrigenòmica)
Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
González, Josefa (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))

Date:	2020
Abstract:	Motivation: Transposable elements (TEs) constitute a significant proportion of the majority of genomes sequenced to date. TEs are responsible for a considerable fraction of the genetic variation within and among species. Accurate genotyping of TEs in genomes is therefore crucial for a complete identification of the genetic differences among individuals, populations and species. Results: In this work, we present a new version of T-lex, a computational pipeline that accurately genotypes and estimates the population frequencies of reference TE insertions using short-read high-throughput sequencing data. In this new version, we have re-designed the T-lex algorithm to integrate the BWA-MEM short-read aligner, which is one of the most accurate short-read mappers and can be launched on longer short-reads (e. g. reads.
Grants:	European Commission 647900 Agència de Gestió d'Ajuts Universitaris i de Recerca 2017/SGR-880 Agencia Estatal de Investigación AGL2016-78992-R
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Published in:	Bioinformatics, Vol. 36, Issue 4 (February 2020) , p. 1191-1197, ISSN 1367-4811

DOI: 10.1093/bioinformatics/btz727
PMID: 31580402

7 p, 1.9 MB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles