ArticleBioinformatics (Oxford, England)2014
MindTheGap: integrated detection and assembly of short and long insertions.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
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- Quaternary Climatic Changes and Biogeographic Barriers Drove Codiversification in the Obligate Mutualism BetweenEcology and evolution · 2026Article
- Independent and repeated acquisition ofRoyal Society open science · 2025Article
- Performance evaluation of structural variation detection using DNBSEQ whole-genome sequencing.BMC genomics · 2025Article
- MTG-Link: leveraging barcode information from linked-reads to assemble specific loci.BMC bioinformatics · 2023Article
- Efficient detection and assembly of non-reference DNA sequences with synthetic long reads.Nucleic acids research · 2022Article
- Impact of host demography and evolutionary history on endosymbiont molecular evolution: A test in carpenter ants (genusEcology and evolution · 2022Article
- Meerkat: An Algorithm to Reliably Identify Structural Variations and Predict Their Forming Mechanisms.Methods in molecular biology (Clifton, N.J.) · 2022Article
- SIns: A Novel Insertion Detection Approach Based on Soft-Clipped Reads.Frontiers in genetics · 2021Article
- Positive selection alone is sufficient for whole genome differentiation at the early stage of speciation process in the fall armyworm.BMC evolutionary biology · 2020Article
- Insertion variants missing in the human reference genome are widespread among human populations.BMC biology · 2020Article
- Towards a better understanding of the low recall of insertion variants with short-read based variant callers.BMC genomics · 2020Article
- MinYS: mine your symbiont by targeted genome assembly in symbiotic communities.NAR genomics and bioinformatics · 2020Article
- Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak.PLoS pathogens · 2020Article
- EXFI: Exon and splice graph prediction without a reference genome.Ecology and evolution · 2020Article
- Structural variants in 3000 rice genomes.Genome research · 2019Article
- Identification and manipulation ofBiotechnology for biofuels · 2019Article
- Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches.Microbiome · 2018Article
- Discovery and genotyping of novel sequence insertions in many sequenced individuals.Bioinformatics (Oxford, England) · 2017Article
- Variant genotyping with gap filling.PloS one · 2017Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationInsertions play an important role in genome evolution. However, such variants are difficult to detect from short-read sequencing data, especially when they exceed the paired-end insert size. Many approaches have been proposed to call short insertion variants based on paired-end mapping. However, there remains a lack of practical methods to detect and assemble long variants.
resultsWe propose here an original method, called MindTheGap, for the integrated detection and assembly of insertion variants from re-sequencing data. Importantly, it is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. MindTheGap uses an efficient k-mer-based method to detect insertion sites in a reference genome, and subsequently assemble them from the donor reads. MindTheGap showed high recall and precision on simulated datasets of various genome complexities. When applied to real Caenorhabditis elegans and human NA12878 datasets, MindTheGap detected and correctly assembled insertions >1 kb, using at most 14 GB of memory.
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