ArticleNucleic acids research2013
Detecting Alu insertions from high-throughput sequencing data.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Article
- Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.Life (Basel, Switzerland) · 2022Review
- AluMine: alignment-free method for the discovery of polymorphic Alu element insertions.Mobile DNA · 2019Article
- Article
- Computational tools to unmask transposable elements.Nature reviews. Genetics · 2018Review
- Discovery of rare, diagnosticMobile DNA · 2017Article
- A polymorphic Alu insertion that mediates distinct disease-associated deletions.European journal of human genetics : EJHG · 2016Article
- Discovery and characterization of Alu repeat sequences via precise local read assembly.Nucleic acids research · 2015Article
- The Wukong Terminal-Repeat Retrotransposon in Miniature (TRIM) Elements in Diverse Maize Germplasm.G3 (Bethesda, Md.) · 2015Article
- Article
- Assembly and characterization of novelMobile genetic elements · 2014Article
- MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.PloS one · 2014Article
- Mobster: accurate detection of mobile element insertions in next generation sequencing data.Genome biology · 2014Article
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Authors and funding
3 authors.
Funding
Abstract
High-throughput sequencing technologies have allowed for the cataloguing of variation in personal human genomes. In this manuscript, we present alu-detect, a tool that combines read-pair and split-read information to detect novel Alus and their precise breakpoints directly from either whole-genome or whole-exome sequencing data while also identifying insertions directly in the vicinity of existing Alus. To set the parameters of our method, we use simulation of a faux reference, which allows us to compute the precision and recall of various parameter settings using real sequencing data. Applying our method to 100 bp paired Illumina data from seven individuals, including two trios, we detected on average 1519 novel Alus per sample. Based on the faux-reference simulation, we estimate that our method has 97% precision and 85% recall. We identify 808 novel Alus not previously described in other studies. We also demonstrate the use of alu-detect to study the local sequence and global location preferences for novel Alu insertions.
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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.