ArticleProceedings of the National Academy of Sciences of the United States of America2013
Reference-assisted chromosome assembly.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
76 citing papers in PubMed.
- Identification and characterization of low-sulfur-inducible genes and pathways in roots of upland and lowland rice grown under hydroponic and soil conditions.Journal of experimental botany · 2026Article
- MGA: a tool for haplotype-mixed assembly of long and accurate reads.Genome biology · 2026Article
- Article
- Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity.Ecology and evolution · 2025Article
- A chromosome-level genome assembly of the Korean minipig (Sus scrofa).Scientific data · 2024Article
- Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.Cell · 2024Article
- The Utilization of Reference-Guided Assembly and In Silico Libraries Improves the Draft Genome of Clarias batrachus and Culter alburnus.Marine biotechnology (New York, N.Y.) · 2023Article
- Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human.Scientific reports · 2023Article
- A chromosome-level genome assembly of the Korean crossbred pig Nanchukmacdon (Sus scrofa).Scientific data · 2023Article
- Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights.BMC genomics · 2023Article
- Anemonefishes: A model system for evolutionary genomics.F1000Research · 2023Review
- Assembly of complete diploid-phased chromosomes from draft genome sequences.G3 (Bethesda, Md.) · 2022Article
- Article
- Recombination Marks the Evolutionary Dynamics of a Recently Endogenized Retrovirus.Molecular biology and evolution · 2021Article
- SWALO: scaffolding with assembly likelihood optimization.Nucleic acids research · 2021Article
- PromethION Sequencing and Assembly of the Genome of Micropoecilia picta, a Fish with a Highly Degenerated Y Chromosome.Genome biology and evolution · 2021Article
- Extreme Y chromosome polymorphism corresponds to five male reproductive morphs of a freshwater fish.Nature ecology & evolution · 2021Article
- Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ.Nature communications · 2020Article
- Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma).BMC genomics · 2020Article
- Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
Abstract
One of the most difficult problems in modern genomics is the assembly of full-length chromosomes using next generation sequencing (NGS) data. To address this problem, we developed "reference-assisted chromosome assembly" (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads. Evaluation of results using simulated and real genome assemblies indicates that our approach can substantially improve genomes generated by a wide variety of de novo assemblers if a good reference assembly of a closely related species and outgroup genomes are available. We used RACA to reconstruct 60 Tibetan antelope (Pantholops hodgsonii) chromosome fragments from 1,434 SOAPdenovo sequence scaffolds, of which 16 chromosome fragments were homologous to complete cattle chromosomes. Experimental validation by PCR showed that predictions made by RACA are highly accurate. Our results indicate that RACA will significantly facilitate the study of chromosome evolution and genome rearrangements for the large number of genomes being sequenced by NGS that do not have a genetic or physical map.
Indexed as
Identifiers
What OpenQuestion holds
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.