ArticleGigaScience2018
Improving draft genome contiguity with reference-derived in silico mate-pair libraries.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed.
- Genomic signatures of climate adaptation in bank voles.Ecology and evolution · 2024Article
- Optimization of the "Ecology and evolution · 2023Article
- Phylogenomic analysis of the bowfin (Amia calva) reveals unrecognized species diversity in a living fossil lineage.Scientific reports · 2022Article
- Article
- Comparative analysis of draft genome assemblies developed from whole genome sequences of twoBiotechnology reports (Amsterdam, Netherlands) · 2021Article
- Diversity and Paleodemography of the Addax (Genes · 2021Article
- Ocean-wide genomic variation in Gray's beaked whales,Royal Society open science · 2021Article
- Toward a more holistic method of genome assembly assessment.BMC bioinformatics · 2020Review
- Refinement of Draft Genome Assemblies of Pigeonpea (Frontiers in genetics · 2020Article
- Article
- Narwhal Genome Reveals Long-Term Low Genetic Diversity despite Current Large Abundance Size.iScience · 2019Article
- Genomic analyses reveal an absence of contemporary introgressive admixture between fin whales and blue whales, despite known hybrids.PloS one · 2019Article
- Improving draft genome contiguity with reference-derived in silico mate-pair libraries.GigaScience · 2018Article
- ImproveAssembly - Tool for identifying new gene products and improving genome assembly.PloS one · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Background: Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available. Findings: In order to improve genome contiguity, we have developed Cross-Species Scaffolding-a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico. Conclusions: We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ∼30x coverage of shotgun sequencing data.
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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.