Orienting Ordered Scaffolds: Complexity and Algorithms

Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose order and/or orientation (i.e., strand) in the genome are unknown. There exist various scaffold assembly methods, which attempt to determine the order and orientation of scaffolds along the genome chromosomes. Some of these methods (e.g., based on FISH physical mapping, chromatin conformation capture, etc.) can infer the order of scaffolds, but not necessarily their orientation. This leads to a special case of the scaffold orientation problem (i.e., deducing the orientation of each scaffold) with a known order of the scaffolds. We address the problem of orientating ordered scaffolds as an optimization problem based on given weighted orientations of scaffolds and their pairs (e.g., coming from pair-end sequencing reads, long reads, or homologous relations). We formalize this problem using notion of a scaffold graph (i.e., a graph, where vertices correspond to the assembled contigs or scaffolds and edges represent connections between them). We prove that this problem is NP-hard, and present a polynomial-time algorithm for solving its special case, where orientation of each scaffold is imposed relatively to at most two other scaffolds. We further develop an FPT algorithm for the general case of the OOS problem

Effects of differently sequenced classroom scripts on transformative and regulative processes in inquiry learning

Kooperatives Forschendes Lernen hat sich empirisch als ein effektiver Instruktionsansatz für die Förderung des naturwissenschaftlichen Denkens bewährt. Obwohl Forschung zur Orchestrierung von Sozialformen im Unterricht zeigt, dass diese einen wichtigen Einfluss auf die Qualität von Lernprozessen, wie Kommunikations- und Interaktionsprozessen, und damit auf die Lernergebnisse von Gruppe und einzelnen Lernenden hat, wurde im Bereich des Forschenden Lernens die Verteilung und Abfolge von individuellen und kooperativen Lernaktivitäten bislang jedoch kaum untersucht. Basierend auf Erkenntnissen zu Scaffolding, Fading, Productive Failure und dem ICAP-Rahmenmodell wird in der vorliegenden Arbeit der Einfluss zweier Unterrichtsskripts auf die transformativen und regulativen Prozesse des forschenden Lernens bei Individuen und Gruppen untersucht. Das eine Unterrichtsskript sieht die Abfolge „Plenum-Kleingruppe-Individuum“ vor (PKI-Skript), das andere wechselt vom Plenum über die individuelle Ebene zur Kleingruppenebene (PIK-Skript). Transformationsprozesse beziehen sich dabei auf wissensgenerierende Prozesse, während regulative Prozesse meta-kognitive Prozesse darstellen. Deskriptiv zeigten sich unterschieden zwischen den beiden Bedingungen: Lernende mit dem PKI-Skript zeigten mehr und intensivere individuelle transformative Prozesse, z.B. während bei der Datenauswertung und beim wissenschaftlichen Schlussfolgern. Lernende mit dem PIK-Skript zeigten hingegen mehr transformative und regulative Prozessen auf der Gruppenebene. Lernende, die mit diesem Skript arbeiteten, zeigten mehr und intensivere Grounding-Aktivitäten, die das gemeinsame Verständnis und das Entstehen eines Common Ground förderten. Dementsprechend zeigten sich hier auch häufiger intensivere transformative Prozesse auf der Gruppenebene.Collaborative inquiry learning has been empirically proven to be an effective instructional approach to foster students’ scientific literacy. However, there is little research on the coordination of individual and collaborative activities during inquiry learning which could shape the quality of communication and interaction, and consequentially, individual and group learning outcomes. Research has indicated that classroom orchestration (i.e., distribution and sequencing of activities) could have profound effect on learning processes and outcomes. Premised on theories of scaffolding, fading, productive failure and the ICAP (interactive, constructive, active and passive) framework on different activity types, this study investigates the effects of two differently sequenced classroom scripts on the individual and group transformative and regulative processes in inquiry learning. Transformative processes refers to processes that yield knowledge and regulative processes are meta-cognitive processes. Descriptive statistics suggest that the Plenary-Small Group-Individual (PSI) script transition facilitated better individual engagement in transformative processes such as generating of evidence and the drawing of conclusions, whereas the Plenary-Individual-Small Group (PIS) script condition fostered better transformative and regulative processes for the group. Establishing shared understanding and forging common grounds through grounding and high-level grounding was more prevalent in this script condition, which also accounted for more occurrences of high-level transformative processes at the group level

A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome

The high degree of polymorphism in the genome of the sea squirt Ciona savignyi complicated the assembly of sequence contigs, but a new alignment method results in a much improved sequence

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules

ntLink: a toolkit for de novo genome assembly scaffolding and mapping using long reads

With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the generation of high-quality genome assemblies in a computationally efficient manner are essential. Recent developments in long-read sequencing technologies have greatly benefited genome assembly work, including scaffolding, by providing long-range evidence that can aid in resolving the challenging repetitive regions of complex genomes. ntLink is a flexible and resource-efficient genome scaffolding tool that utilizes long-read sequencing data to improve upon draft genome assemblies built from any sequencing technologies, including the same long reads. Instead of using read alignments to identify candidate joins, ntLink utilizes minimizer-based mappings to infer how input sequences should be ordered and oriented into scaffolds. Recent improvements to ntLink have added important features such as overlap detection, gap-filling and in-code scaffolding iterations. Here, we present three basic protocols demonstrating how to use each of these new features to yield highly contiguous genome assemblies, while still maintaining ntLink's proven computational efficiency. Further, as we illustrate in the alternate protocols, the lightweight minimizer-based mappings that enable ntLink scaffolding can also be utilized for other downstream applications, such as misassembly detection. With its modularity and multiple modes of execution, ntLink has broad benefit to the genomics community, from genome scaffolding and beyond. ntLink is an open-source project and is freely available from https://github.com/bcgsc/ntLink.Comment: 23 pages, 2 figure

A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A

Citation: Balcarkova, B., Frenkel, Z., Skopova, M., Abrouk, M., Kumar, A., Chao, S. M., . . . Valarik, M. (2017). A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A. Frontiers in Plant Science, 7, 14. https://doi.org/10.3389/fpls.2016.02063Bread wheat has a large and complex allohexaploid genome with low recombination level at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers, contigs of physical maps and sequence scaffolds and impedes obtaining of high-quality reference genome sequence. Here we report on the construction of high-density and high-resolution radiation hybrid (RH) map of chromosome 4A supported by high-density chromosome deletion map. A total of 119 endosperm-based RH lines of two RH panels and 15 chromosome deletion bin lines were genotyped with 90K iSelect single nucleotide polymorphism (SNP) array. A total of 2316 and 2695 markers were successfully mapped to the 4A RH and deletion maps, respectively. The chromosome deletion map was ordered in 19 bins and allowed precise identification of centromeric region and verification of the RH panel reliability. The 4A-specific RH map comprises 1080 mapping bins and spans 6550.9 cR with a resolution of 0.13 Mb/cR. Significantly higher mapping resolution in the centromeric region was observed as compared to recombination maps. Relatively even distribution of deletion frequency along the chromosome in the RH panel was observed and putative functional centromere was delimited within a region characterized by two SNP markers

Genome scaffolding using poled clone sequencing

Ankara : The Department of Computer Engineering and the Graduate School of Engineering and Science of Bilkent University, 2014.Thesis (Master's) -- Bilkent University, 2014.Includes bibliographical references leaves 49-53.The DNA sequencing technologies hold great promise in generating information that will guide scientists to learn more about how the genome affects human health, organismal evolution, and genetic relationships between individuals of the same species. The process of generating raw genome sequence data becomes cheaper, faster, but more error prone. Assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ in terms of their performance, and in their final output. More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. In this thesis, we evaluated the accuracies of several genome scaffolding algorithms using two different types of data generated from the genome of the same human individual: i) whole genome shotgun sequencing (WGS), and ii) pooled clone sequencing (PCS). We observed that, it is possible to obtain less number of scaffolds with longer total assemble length if PCS data is used, compared to using only WGS data. However, the current scaffolding algorithms are developed only for WGS, and PCS-aware scaffolding algorithms remain an open problem.Dal, ElifM.S