ArticleBMC genomics2013
Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.Cell genomics · 2024Article
- A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.bioRxiv : the preprint server for biology · 2023Article
- Optimization of the "Ecology and evolution · 2023Article
- Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication.BMC genomics · 2020Article
- IMA Genome - F13: Draft genome sequences ofIMA fungus · 2020Article
- Development of coupling controlled polymerizations by adapter-ligation in mate-pair sequencing for detection of various genomic variants in one single assay.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary.Molecular ecology resources · 2019Article
- Prenatal Diagnosis of Fetuses With Increased Nuchal Translucency by Genome Sequencing Analysis.Frontiers in genetics · 2019Article
- Location of Balanced Chromosome-Translocation Breakpoints by Long-Read Sequencing on the Oxford Nanopore Platform.Frontiers in genetics · 2019Article
- Improving draft genome contiguity with reference-derived in silico mate-pair libraries.GigaScience · 2018Article
- Single-Molecule Sequencing of theG3 (Bethesda, Md.) · 2017Article
- Genomic survey sequencing for development and validation of single-locus SSR markers in peanut (Arachis hypogaea L.).BMC genomics · 2016Article
- Greater thanPeerJ · 2016Article
- Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis.Scientific reports · 2015Article
- Genomic landscape of rat strain and substrain variation.BMC genomics · 2015Article
- Complete Genome Sequence of Thermus aquaticus Y51MC23.PloS one · 2015Article
- Review
- Detection of chromosomal breakpoints in patients with developmental delay and speech disorders.PloS one · 2014Article
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Authors and funding
12 authors.
Funding
Abstract
backgroundPaired-tag sequencing approaches are commonly used for the analysis of genome structure. However, mammalian genomes have a complex organization with a variety of repetitive elements that complicate comprehensive genome-wide analyses.
resultsHere, we systematically assessed the utility of paired-end and mate-pair (MP) next-generation sequencing libraries with insert sizes ranging from 170 bp to 25 kb, for genome coverage and for improving scaffolding of a mammalian genome (Rattus norvegicus). Despite a lower library complexity, large insert MP libraries (20 or 25 kb) provided very high physical genome coverage and were found to efficiently span repeat elements in the genome. Medium-sized (5, 8 or 15 kb) MP libraries were much more efficient for genome structure analysis than the more commonly used shorter insert paired-end and 3 kb MP libraries. Furthermore, the combination of medium- and large insert libraries resulted in a 3-fold increase in N50 in scaffolding processes. Finally, we show that our data can be used to evaluate and improve contig order and orientation in the current rat reference genome assembly.
conclusionsWe conclude that applying combinations of mate-pair libraries with insert sizes that match the distributions of repetitive elements improves contig scaffolding and can contribute to the finishing of draft genomes.
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