ReviewGigaScience2014
Computational methods for optical mapping.
Review in GigaScience, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed.
- Pasa: leveraging population pangenome graph to scaffold prokaryote genome assemblies.Nucleic acids research · 2024Article
- OM2Seq: learning retrieval embeddings for optical genome mapping.Bioinformatics advances · 2024Article
- Design of optimal labeling patterns for optical genome mapping via information theory.Bioinformatics (Oxford, England) · 2023Article
- LongStitch: high-quality genome assembly correction and scaffolding using long reads.BMC bioinformatics · 2021Article
- Article
- Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale.Essays in biochemistry · 2021Article
- Signal-based optical map alignment.PloS one · 2021Article
- Identifying microbial species by single-molecule DNA optical mapping and resampling statistics.NAR genomics and bioinformatics · 2020Article
- Advances in optical mapping for genomic research.Computational and structural biotechnology journal · 2020Review
- Re-sequencing and optical mapping reveals misassemblies and real inversions on Corynebacterium pseudotuberculosis genomes.Scientific reports · 2019Article
- Modern technologies and algorithms for scaffolding assembled genomes.PLoS computational biology · 2019Review
- Piercing the dark matter: bioinformatics of long-range sequencing and mapping.Nature reviews. Genetics · 2018Review
- Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach.PloS one · 2018Article
- OMBlast: alignment tool for optical mapping using a seed-and-extend approach.Bioinformatics (Oxford, England) · 2017Article
- Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences.The Plant cell · 2016Article
- OMWare: a tool for efficient assembly of genome-wide physical maps.BMC bioinformatics · 2016Article
- PEPR: pipelines for evaluating prokaryotic references.Analytical and bioanalytical chemistry · 2016Article
- OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis.GigaScience · 2016Article
- The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes.Mammalian genome : official journal of the International Mammalian Genome Society · 2015Article
- Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool.BMC genomics · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Optical mapping and newer genome mapping technologies based on nicking enzymes provide low resolution but long-range genomic information. The optical mapping technique has been successfully used for assessing the quality of genome assemblies and for detecting large-scale structural variants and rearrangements that cannot be detected using current paired end sequencing protocols. Here, we review several algorithms and methods for building consensus optical maps and aligning restriction patterns to a reference map, as well as methods for using optical maps with sequence assemblies.
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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.