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- Bradnam, K. R., et al.
(author)
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Assemblathon 2 : Evaluating de novo methods of genome assembly in three vertebrate species
- 2013
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In: GigaScience. - : BioMed Central (BMC). - 2047-217X. ; 2:1
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Journal article (peer-reviewed)abstract
- Background: The 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. Results: In 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. Conclusions: Many 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.
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| 2. |
- Chikhi, N., et al.
(author)
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Evaluation of an effective diameter to study quenching and dry-out of complex debris bed
- 2014
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In: Annals of Nuclear Energy. - : Elsevier BV. - 0306-4549 .- 1873-2100. ; 74, s. 24-41
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Journal article (peer-reviewed)abstract
- Many of the current research works performed in the SARNET-2 WP5 deal with the study of the coolability of debris beds in case of severe nuclear power plant accidents. One of the difficulties for modeling and transposition of experimental results to the real scale and geometry of a debris bed in a reactor is the difficulty to perform experiments with debris beds that are representative for reactor situations. Therefore, many experimental programs have been performed using beds made of multi-diameter spheres or non-spherical particles to study the physical phenomena involved in debris bed coolability and to evaluate an effective diameter. This paper first establishes the ranges of porosity and particle size distribution that might be expected for in-core debris beds and ex-vessel debris beds. Then, the results of pressure drop and dry-out heat flux (DHF) measurements obtained in various experimental setups, POMECO, DEBRIS, COOLOCE/STYX and CALIDE/PRELUDE, are presented. The issues of particle size distribution and non-sphericity are also investigated. It is shown that the experimental data obtained in "simple" debris beds are relevant to describe the behavior of more complex beds. Indeed, for several configurations, it is possible to define an "effective" diameter suitable for evaluating (with the porosity) some model parameters as well as correlations for the pressure drop across the bed, the steam flow rate during quenching and the DHF.
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| 3. |
- Pires, Ana Elisabete, et al.
(author)
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The curious case of the Mesolithic Iberian dogs : An archaeogenetic study
- 2019
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In: Journal of Archaeological Science. - : Elsevier BV. - 0305-4403 .- 1095-9238. ; 105, s. 116-129
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Journal article (peer-reviewed)abstract
- We investigated the genetic composition of six Canis remains from western Iberia, directly radiocarbon dated to 7,903-7,570 years (cal BP). They were identified as dogs via their archaeological and depositional context, osteometry, and a high percentage of aquatic diet shared with humans. For comparison, genetic data were obtained from an additional 37 Iberian dog remains from the Neolithic to Late Antiquity, as well as two Palaeolithic and a Chalcolithic Canis identified as wolves. Previous data indicated that dog mtDNA haplogroup A (HgA) is prevalent in extant European dogs ( > 50%), in the Near East and Asia, but rare or absent ( < 10%) in European Canis older than 3,000 years (cal BP). We found a high frequency (83%) of dog HgA in Mesolithic Iberian dog remains. This is the first report of a high frequency of dog HgA in pre-Neolithic Europe. We show that, contrary to the current view, Canis with HgA did not necessarily arrive in Europe from East-Asia. This phylogeographical difference in HgA frequency demonstrates that genetic differentiation was high prior to, or as a consequence of, domestication which may be linked with pre-Neolithic local processes for Iberian wolf domestication. Our results emphasize that knowledge of both ancient wolves' and early dogs' genetic profiles from the European periphery should improve our understanding of the evolution of the European dog.
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