Readfish enables targeted nanopore sequencing of gigabase-sized genomes

© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Nanopore sequencers can be used to selectively sequence certain DNA molecules in a pool by reversing the voltage across individual nanopores to reject specific sequences, enabling enrichment and depletion to address biological questions. Previously, we achieved this using dynamic time warping to map the signal to a reference genome, but the method required substantial computational resources and did not scale to gigabase-sized references. Here we overcome this limitation by using graphical processing unit (GPU) base-calling. We show enrichment of specific chromosomes from the human genome and of low-abundance organisms in mixed populations without a priori knowledge of sample composition. Finally, we enrich targeted panels comprising 25,600 exons from 10,000 human genes and 717 genes implicated in cancer, identifying PML–RARA fusions in the NB4 cell line i

Phasage d’haplotypes par ASP à partir de longues lectures : une approche d’optimisation flexible

Version non corrigée. Une nouvelle version sera disponible d'ici mars 2023.Each chromosome of a di- or polyploid organism has several haplotypes, which are highly similar but diverge on a certain number of positions. However, most of the reference genomes only provide a single sequence for each chromosome, and therefore do not reflect the biological reality.Yet, it is crucial to have access to this information, which is useful in medicine, agronomy and population studies. The recent development of third generation technologies, especially PacBio and Oxford Nanopore Technologies sequencers, has allowed for the production of long reads that facilitate haplotype sequence reconstruction.Bioinformatics methods exist for this task, but they provide only a single solution. This thesis introduces an approach for haplotype phasing based on the search of connected components in a read similarity graph to identify haplotypes. This method uses Answer Set Programming to work on the set ofoptimal solutions. This phasing algorithm has been used to reconstruct haplotypes of the diploid rotifer Adineta vaga.Chaque chromosome d’organisme di- ou polyploïde présente plusieurs haplotypes, qui sont fortement similaires mais divergent sur un certain nombre de positions. Cependant, la majorité des génomes de référence ne renseignent qu’une seule séquence pour chaque chromosome, et ne reflètent donc pas la réalité biologique. Or, il est crucial d’avoir accès à ces informations, qui sont utiles en médecine, en agronomie ou encore dans l’étude des populations. Le récent développement des technologies de troisième génération, notamment des séquenceurs PacBio et Oxford NanoporeTechnologies, a permis la production de lectures longues facilitant la reconstruction des séquences d’haplotypes. Il existe pour cela des méthodes bioinformatiques, mais elles ne fournissent qu’une unique solution. Cette thèse propose une méthode de phasage d’haplotype basée sur la recherchede composantes connexes dans un graph de similarité des lectures pour identifier les haplotypes. Cette méthode utilise l’Answer Set Programming pour travailler sur l’ensemble des solutions optimales. L’algorithme de phasage a permis de reconstruire les haplotypes du rotifère diploïde Adineta vaga

ACARORUM CATALOGUS IX. Acariformes, Acaridida, Schizoglyphoidea (Schizoglyphidae), Histiostomatoidea (Histiostomatidae, Guanolichidae), Canestrinioidea (Canestriniidae, Chetochelacaridae, Lophonotacaridae, Heterocoptidae), Hemisarcoptoidea (Chaetodactylidae, Hyadesiidae, Algophagidae, Hemisarcoptidae, Carpoglyphidae, Winterschmidtiidae)

The 9th volume of the series Acarorum Catalogus contains lists of mites of 13 families, 225 genera and 1268 species of the superfamilies Schizoglyphoidea, Histiostomatoidea, Canestrinioidea and Hemisarcoptoidea. Most of these mites live on insects or other animals (as parasites, phoretic or commensals), some inhabit rotten plant material, dung or fungi. Mites of the families Chetochelacaridae and Lophonotacaridae are specialised to live with Myriapods (Diplopoda). The peculiar aquatic or intertidal mites of the families Hyadesidae and Algophagidae are also included.Publishe

3rd International Workshop on Instrumentation for Planetary Missions : October 24–27, 2016, Pasadena, California

The purpose of this workshop is to provide a forum for collaboration, exchange of ideas and information, and discussions in the area of the instruments, subsystems, and other payload-related technologies needed to address planetary science questions. The agenda will compose a broad survey of the current state-of-the-art and emerging capabilities in instrumentation available for future planetary missions.Universities Space Research Association (USRA); Lunar and Planetary Institute (LPI); Jet Propulsion Laboratory (JPL)Conveners: Sabrina Feldman, Jet Propulsion Laboratory, David Beaty, Jet Propulsion Laboratory ; Science Organizing Committee: Carlton Allen, Johnson Space Center (retired) [and 12 others

2015 Oklahoma Research Day Full Program

This document contains all abstracts from the 2015 Oklahoma Research Day held at Northeastern State University

Reproductive and molecular ecology of the European lobster: Implications for conservation management

The European lobster (Homarus gammarus) is an ecologically important benthic decapod which supports fisheries that are critical to the economic prosperity of coastal communities. However, populations across its range are pressured by rising exploitation, from which management has failed to prevent stock collapses in the recent past. Fisheries management of the species is significantly hindered by deficiencies in our knowledge of fundamental characteristics of population biology, including the connectivity and genetic diversity of stocks. As a result, the effectiveness of strategies designed to conserve recruitment and ensure harvests are sustainable is poorly understood. This thesis focuses on elucidating aspects of reproductive and molecular ecology in H. gammarus which can be used to inform and appraise conservation management initiatives, currently applied via both the regulation of capture and the wild release of hatchery-reared juveniles. The size-specific fecundity of reproducing females was defined around southwestern UK, and spatial variation in clutch size between populations was linked to a longitudinal gradient in oceanic temperature range across Northern Europe. The reconstruction of paternal genotypes show that single males fertilise individual clutches, which hints at demographic stability within a productive Atlantic fishery. Population genetic structure, investigated at a fine spatial scale in the same region, evidenced high connectivity and suggests that the localised interventions of an active hatchery do not lead to juveniles being released beyond areas they might naturally recruit via planktonic dispersal. However, genetic differentiation and isolation-by-distance at a broad geographic scale indicate that direct gene flow between remote populations is limited, so that (i) a failure to maintain spawning stock biomass may negatively affect local recruitment, (ii) the utilisation of non-resident broodstock for hatchery stocking may cause a loss of adaptive potential, and (iii) the recovery of depleted stocks is likely to be problematic. Finally, simulations indicated that genetic parentage assignment will prove accurate in distinguishing cultured individuals from natural stock among admixed populations in the wild, an important development that should facilitate the optimisation of hatchery stocking and lead to rigorous assessments of the conservation value of releasing lobsters reared in captivity.European Social FundThe Fishmonger's Compan