Benchmarking computational tools for polymorphic transposable element detection

ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data

(2015) Chuan Jiang et al.   BMC BIOINFORMATICS

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Transposable element polymorphisms recapitulate human evolution

(2015) Lavanya Rishishwar et al.   Mobile DNA

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Transposable element detection from whole genome sequence data

(2015) Adam D. Ewing   Mobile DNA

Tangram: a comprehensive toolbox for mobile element insertion detection

(2014) Jiantao Wu et al.   BMC GENOMICS

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data

(2014) Anna-Sophie Fiston-Lavier et al.   NUCLEIC ACIDS RESEARCH

TEMP: a computational method for analyzing transposable element polymorphism in populations

(2014) Jiali Zhuang et al.   NUCLEIC ACIDS RESEARCH

RetroSeq: transposable element discovery from next-generation sequencing data

(2012) Thomas M. Keane et al.   BIOINFORMATICS

Active human retrotransposons: variation and disease

(2012) Dustin C Hancks et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

LINE-1 Elements in Structural Variation and Disease

(2011) Christine R. Beck et al.   Annual Review of Genomics and Human Genetics

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Reading TE leaves: New approaches to the identification of transposable element insertions

(2011) D. A. Ray et al.   GENOME RESEARCH

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS