ArticleGigaScience2013
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
Article in GigaScience, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 344 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
344 citing papers in PubMed.
- Snail plots are badges of genome assembly quality.G3 (Bethesda, Md.) · 2026Article
- Genetic Diversity and Population Structure of the Black-Footed Cat: Insights intobioRxiv : the preprint server for biology · 2026Article
- In Silico Analysis of Polycyclic Aromatic Hydrocarbon (PAH) Degrader fromCurrent issues in molecular biology · 2026Article
- PAQman: reference-free ensemble evaluation of long-read genome assemblies.G3 (Bethesda, Md.) · 2026Article
- A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana.G3 (Bethesda, Md.) · 2026Article
- High-quality chromosome-scale genome assemblies of 29 maize inbred lines of European breeding relevance.Scientific data · 2026Article
- Fine-mapping, candidate gene identification, and marker development for the apple scab resistance gene Rvi2.Journal of experimental botany · 2026Article
- Rapid genome modifications including chromosomal fusions and large-scale inversions are key features in Arctic codfish species.Genome biology · 2026Article
- Article
- Oral Microbiome in Oral Cancer Research from Sampling to Analysis: Strategies, Challenges, and Recommendations.Cancers · 2025Review
- DVOUG enables robust DNA sequence assembly and reconstruction with a dynamic, variable-order graph.Cell reports methods · 2025Article
- A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector.Nature protocols · 2025Review
- Chromosome-level assembly of the 400-year-old Goethe's Palm (Chamaerops humilis L.).Scientific data · 2025Article
- New Genome Assemblies for Poeciliidae: A Foundation for Adaptation Studies.Genome biology and evolution · 2025Article
- Mechanisms underlying the loss of migratory behaviour in a long-lived bird.The Journal of animal ecology · 2025Article
- Characterisation of the Gillenia S-locus provides insight into evolution of the nonself-recognition self-incompatibility system in apple.Scientific reports · 2025Article
- Parameterizing Pantherinae: De Novo Mutation Rate Estimates from Panthera and Neofelis Pedigrees.Genome biology and evolution · 2025Article
- Selection on the vascular-remodelingEvolution letters · 2025Article
- Haplotype-resolved genome assembly of Ficus carica L. reveals allele-specific expression in the fruit.The Plant journal : for cell and molecular biology · 2025Article
- Using reinforcement learning in genome assembly: in-depth analysis of a Q-learning assembler.Frontiers in bioinformatics · 2025Article
284 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
91 authors.
Funding
Abstract
backgroundThe process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly.
resultsIn Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies.
conclusionsMany current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
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.