Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for columbids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for 2 columbid species, Columba livia and Columba guinea. We simultaneously assembled C. livia and C. guinea genomes from long-read sequencing of a single F1 hybrid individual. The new C. livia genome assembly (Cliv_3) shows improved completeness and contiguity relative to Cliv_2.1, with an annotation incorporating long-read IsoSeq data for more accurate gene models. Intensive selective breeding of C. livia has given rise to hundreds of breeds with diverse morphological and behavioral characteristics, and Cliv_3 offers improved tools for mapping the genomic architecture of interesting traits. The C. guinea genome assembly is the first for this species and is a new resource for avian comparative genomics. Together, these assemblies and annotations provide improved resources for functional studies of columbids and avian comparative genomics in general.

Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for colubids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for two columbid species, Columba livia and C. guinea. We simultaneously assembled C. livia and C. guinea genomes from long-read sequencing of a single F1 hybrid individual. The new C. livia genome assembly (Cliv_3) shows improved completeness and contiguity relative to Cliv_2.1, with an annotation incorporating long-read IsoSeq data for more accurate gene models. Intensive selective breeding of C. livia has given rise to hundreds of breeds with diverse morphological and behavioral characteristics, and Cliv_3 offers improved tools for mapping the genomic architecture of interesting traits. The C. guinea genome assembly is the first for this species and is a new resource for avian comparative genomics. Together, these assemblies and annotations provide improved resources for functional studies of columbids and avian comparative genomics in general.

ABSTRACT Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for colubids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for two columbid species, Columba livia and C. guinea . We simultaneously assembled C. livia and C. guinea genomes from long-read sequencing of a single F 1 hybrid individual. The new C. livia genome assembly (Cliv_3) shows improved completeness and contiguity relative to Cliv_2.1, with an annotation incorporating long-read IsoSeq data for more accurate gene models. Intensive selective breeding of C. livia has given rise to hundreds of breeds with diverse morphological and behavioral characteristics, and Cliv_3 offers improved tools for mapping the genomic architecture of interesting traits. The C. guinea genome assembly is the first for this species and is a new resource for avian comparative genomics. Together, these assemblies and annotations provide improved resources for functional studies of columbids and avian comparative genomics in general. ARTICLE SUMMARY Pigeons and doves are important models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Here, we present high-quality reference genome assemblies and annotations for two pigeon species, the domestic rock pigeon ( Columba livia ) and the African speckled pigeon ( C. guinea ). These assemblies and annotations provide improved resources for both comparative genomics and functional studies.

Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first telomere-to-telomere human genome assembly, which resolves complex segmental duplications and large tandem repeats, including centromeric satellite arrays in a complete hydatidiform mole (CHM13). Although derived from highly accurate sequences, evaluation revealed evidence of small errors and structural misassemblies in the initial draft assembly. To correct these errors, we designed a new repeat-aware polishing strategy that made accurate assembly corrections in large repeats without overcorrection, ultimately fixing 51% of the existing errors and improving the assembly quality value from 70.2 to 73.9 measured from PacBio high-fidelity and Illumina k -mers. By comparing our results to standard automated polishing tools, we outline common polishing errors and offer practical suggestions for genome projects with limited resources. We also show how sequencing biases in both high-fidelity and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies.

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of the human genome, which revolutionized the field of genomics. While these drafts and the updates that followed effectively covered the euchromatic fraction of the genome, the heterochromatin and many other complex regions were left unfinished or erroneous. Addressing this remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium has finished the first truly complete 3.055 billion base pair (bp) sequence of a human genome, representing the largest improvement to the human reference genome since its initial release. The new T2T-CHM13 reference includes gapless assemblies for all 22 autosomes plus Chromosome X, corrects numerous errors, and introduces nearly 200 million bp of novel sequence containing 2,226 paralogous gene copies, 115 of which are predicted to be protein coding. The newly completed regions include all centromeric satellite arrays and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies for the first time.

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species 1–4 . To address this issue, the international Genome 10K (G10K) consortium 5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Genome stability in radioresistant bacterium Deinococcus radiodurans depends on RecA, the main bacterial recombinase. Without RecA, gross genome rearrangements occur during repair of DNA double-strand breaks. Long repeated (insertion) sequences have been identified as hot spots for ectopic recombination leading to genome rearrangements, and single-strand annealing (SSA) postulated to be the most likely mechanism involved in this process. Here, we have sequenced five isolates of D. radiodurans recA mutant carrying gross genome rearrangements to precisely characterize the rearrangements and to elucidate the underlying repair mechanism. The detected rearrangements consisted of large deletions in chromosome II in all the sequenced recA isolates. The mechanism behind these deletions clearly differs from the classical SSA; it utilized short (4–11 bp) repeats as opposed to insertion sequences or other long repeats. Moreover, it worked over larger linear DNA distances from those previously tested. Our data are most compatible with alternative end-joining, a recombination mechanism that operates in eukaryotes, but is also found in Escherichia coli . Additionally, despite the recA isolates being preselected for different rearrangement patterns, all identified deletions were found to overlap in a 35 kb genomic region. We weigh the evidence for mechanistic vs. adaptive reasons for this phenomenon.

In this paper we present Graphmap2, a splice-aware mapper built on our previously developed DNA mapper Graphmap. Graphmap2 is tailored for long reads produced by Pacific Biosciences and Oxford Nanopore devices. It uses several newly developed algorithms which enable higher precision and recall of correctly detected transcripts and exon boundaries. We compared its performance with the state-of-the-art tools Minimap2 and Gmap. On both simulated and real datasets Graphmap2 achieves higher mappability and more correctly recognized exons and their ends. In addition we present an analysis of potential of splice aware mappers and long reads for the identification of previously unknown isoforms and even genes. The Graphmap2 tool is publicly available at https://github.com/lbcb-sci/graphmap2 .

The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource-intensive error-correction and consensus-generation steps to obtain high-quality assemblies. We show that the error-correction step can be omitted and that high-quality consensus sequences can be generated efficiently with a SIMD-accelerated, partial-order alignment-based, stand-alone consensus module called Racon. Based on tests with PacBio and Oxford Nanopore data sets, we show that Racon coupled with miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order of magnitude faster.

Next generation sequencing technologies have made RNA sequencing widely accessible and applicable in many areas of research. In recent years, 3rd generation sequencing technologies have matured and are slowly replacing NGS for DNA sequencing. This paper presents a novel tool for RNA mapping guided by gene annotations. The tool is an adapted version of a previously developed DNA mapper - GraphMap, tailored for third generation sequencing data, such as those produced by Pacific Biosciences or Oxford Nanopore Technologies devices. It uses gene annotations to generate a transcriptome, uses a DNA mapping algorithm to map reads to the transcriptome, and finally transforms the mappings back to genome coordinates. Modified version of GraphMap is compared on several synthetic datasets to the state-of-the-art RNAseq mappers enabled to work with third generation sequencing data. The results show that our tool outperforms other tools in general mapping quality.

During the past ten years, genome sequencing has been an extremely hot and active topic, with an especial momentum happening right now. New, exciting and more affordable technologies have been released, requiring the rapid development of new algorithmic methods to cope with the data. Affordable commercial availability of the sequencing technology and algorithmic methods which can leverage the data could open doors to a vast number of very important applications, such as diagnosis and treatment of chronic diseases through personalized medicine or identification of pathogenic microorganisms from soil, water, food or tissue samples. Sequencing the entire genome of an organism is a difficult problem, because all sequencing technologies to date have limitations on the length of the molecule that they can read (much smaller than the genomes of a vast majority of organisms). In order to obtain the sequence of an entire genome, reads need to be either stitched together (assembled) in a de novo fashion when the genome of the organism is unknown in advance, or mapped and aligned to the reference genome if one exists (reference assembly or mapping). The main problem in both approaches stems from the repeating regions in the genomes which, if longer than the reads, prevent complete assembly of the genome. The need for technologies that would produce longer reads which could solve the problem of repeating regions has resulted in the advent of new sequencing approaches – the so-called third generation sequencing technologies which currently include two representatives: Pacific Biosciences (PacBio) and Oxford Nanopore. Both technologies are characterized, aside from long reads, by high error rates which existing assembly algorithms of the time were not capable of handling. This caused the development of time-consuming read error correction methods which were applied as a pre- processing step prior to assembly. Instead, the focus of the work conducted in the scope of this thesis is to develop novel methods for de novo DNA assembly from third generation sequencing data, which provide enough sensitivity and precision to completely omit the error-correction phase. Strong focus is put on nanopore data. In the scope of this thesis, four new methods were developed: (I) NanoMark - an evaluation framework for comparison of assembly methods from nanopore sequencing data ; (II) GraphMap - a fast and sensitive mapper for long error- prone reads ; (III) Owler - a sensitive overlapper for third generation sequencing ; and (IV) Racon - a rapid consensus module for correcting raw assemblies. Owler and Racon were used as modules in the development of a novel de novo genome assembler Aracon. The results show that Aracon reduces the overall assembly time by at least 3x and up to even an order of magnitude less compared to the state-of-the-art methods, while retaining comparable or better quality of assembly.

Exploiting the power of nanopore sequencing requires the development of new bioinformatics approaches to deal with its specific error characteristics. We present the first nanopore read mapper (GraphMap) that uses a read-funneling paradigm to robustly handle variable error rates and fast graph traversal to align long reads with speed and very high precision (>95%). Evaluation on MinION sequencing datasets against short and long-read mappers indicates that GraphMap increases mapping sensitivity by at least 15-80%. GraphMap alignments are the first to demonstrate consensus calling with <1 error in 100,000 bases, variant calling on the human genome with 76% improvement in sensitivity over the next best mapper (BWA-MEM), precise detection of structural variants from 100bp to 4kbp in length and species and strain-specific identification of pathogens using MinION reads. GraphMap is available open source under the MIT license at https://github.com/isovic/graphmap.

Present day development of FPGAs enables us to implement even very complex computer architectures of the past with very few resources. Furthermore, they enable prospective electronic engineers, computer designers and computer scientists to experiment with those architectures, to gain experience and primarily to open up new possible perspectives on future computer architecture designs. In this chapter we present an implementation of the Cray-1 computer system on the E2LP platform. The initial publicly available generic FPGA design of the Cray processor was modified to fit the specifications of the E2LP board and the Spartan-6 FPGA. Aside from customizing the original design, a translator for the Cray Assembly Language was developed, as well as a basic bootloader to provide the use of this implementation as a teaching tool. The Cray-1 implementation facilitates a perfect learning setup for students of all levels. It can guide a student from the very basic stages which involve the synthesis and transfer of the Cray-1 design onto the E2LP board up to the embedded software design in a real, comprehensive, and historically industrially very significant Cray Assembly Language. Additionally, many advanced laboratory exercises can be made with the core Cray processor implementation on the E2LP board. The expansion of the Cray-1 design into a Cray-XMP, Cray-2 or some other computer from that series enables deep insight in the correspondence of instruction sets, registers and interdependent timings.

In this chapter we present basic set of laboratory exercises, developed under the Embedded Computer Engineering Learning Platform (E2LP) project, with illustrative laboratory examples covering the embedded engineering learning objectives. In order to satisfy the widest range of learning methods and models and to be successful in supporting different types of students, library of laboratory exercises contains a detailed manual/catalog documentation that for each exercise explains the problem covering by the exercise, provide an overview of the required background theoretical knowledge and lead the student to a solution without revealing the actual steps and decisions he or she must make. The E2LP library has more than 60 open source laboratory exercises ready to be presented to other universities. The exercises could also be used over the e-learning portal. Additionally, the E2LP platform integrates an augmented reality interface for visualizing, simulating and monitoring invisible principles, phenomena and facts in the field of electronics hardware and education details. Interactive graphical user interface for web catalogue, provides easy navigation through content of the library of laboratory exercises and enables platform users to ask for help, give feedback, and in general discuss projects based on the E2LP board.

Recent emergence of nanopore sequencing technology set a challenge for the established assembly methods not optimized for the combination of read lengths and high error rates of nanopore reads. In this work we assessed how existing de novo assembly methods perform on these reads. We benchmarked three non-hybrid (in terms of both error correction and scaffolding) assembly pipelines as well as two hybrid assemblers which use third generation sequencing data to scaffold Illumina assemblies. Tests were performed on several publicly available MinION and Illumina datasets of E. coli K-12, using several sequencing coverages of nanopore data (20x, 30x, 40x and 50x). We attempted to assess the quality of assembly at each of these coverages, to estimate the requirements for closed bacterial genome assembly. Results show that hybrid methods are highly dependent on the quality of NGS data, but much less on the quality and coverage of nanopore data and perform relatively well on lower nanopore coverages. Furthermore, when coverage is above 40x, all non-hybrid methods correctly assemble the E. coli genome, even a non-hybrid method tailored for Pacific Bioscience reads. While it requires higher coverage compared to a method designed particularly for nanopore reads, its running time is significantly lower.

During the past ten years, genome sequencing has been an extremely hot and active topic, with an especial momentum happening right now. New, exciting and more affordable technologies have been released, requiring the rapid development of new algorithmic methods to cope with the data. Affordable commercial availability of the sequencing technology and algorithmic methods which can leverage the data could open doors to a vast number of very important applications, such as diagnosis and treatment of chronic diseases through personalized medicine or identification of pathogenic microorganisms from soil, water, food or tissue samples. Sequencing the entire genome of an organism is a difficult problem, because all sequencing technologies to date have limitations on the length of the molecule that they can read (much smaller than the genomes of a vast majority of organisms). In order to obtain the sequence of an entire genome, reads need to be either stitched together (assembled) in a de novo fashion when the genome of the organism is unknown in advance, or mapped and aligned to the reference genome if one exists (reference assembly or mapping). The main problem in both approaches stems from the repeating regions in the genomes which, if longer than the reads, prevent complete assembly of the genome. The need for technologies that would produce longer reads which could solve the problem of repeating regions has resulted in the advent of new sequencing approaches – the so-called third generation sequencing technologies which currently include two representatives: Pacific Biosciences (PacBio) and Oxford Nanopore. Both technologies are characterized, aside from long reads, by high error rates which existing assembly algorithms of the time were not capable of handling. This caused the development of time-consuming read error correction methods which were applied as a pre-processing step prior to assembly. Instead, the focus of the work conducted in the scope of this thesis is to develop novel methods for de novo DNA assembly from third generation sequencing data, which provide enough sensitivity and precision to completely omit the error-correction phase. Strong focus is put on nanopore data.

The paper considers the conceptual approach for organization of the vertical hierarchical links between the scalable distributed computing paradigms: Cloud Computing, Fog Computing and Dew Computing. In this paper, the Dew Computing is described and recognized as a new structural layer in the existing distributed computing hierarchy. In the existing computing hierarchy, the Dew computing is positioned as the ground level for the Cloud and Fog computing paradigms. Vertical, complementary, hierarchical division from Cloud to Dew Computing satisfies the needs of high- and low-end computing demands in everyday life and work. These new computing paradigms lower the cost and improve the performance, particularly for concepts and applications such as the Internet of Things (IoT) and the Internet of Everything (IoE). In addition, the Dew computing paradigm will require new programming models that will efficiently reduce the complexity and improve the productivity and usability of scalable distributed computing, following the principles of High-Productivity computing.

The IR emissivity of human skin is extremly high and measurements of infrared radiation emitted by the skin can be converted directly into accurate temperature value. This process is known as Body IR Thermography. Skin temperature increase associated with increased vascular flow and increased metabolism. In this paper a novel multi-resolution real-time 3D thermal imaging system as potential solution for a human body 3D thermal models standardisation is presented. The system consists of a high-resolution offline 3D scanner and a real-time low-resolution 3D scanner, both of them paired together with a thermal imaging camera. The emphasis of this paper is the presentation of the novel concept of the standardisation of human body 3D thermal models, captured by the multi-resolution real-time 3D thermal imaging system. The standardisation procedure utilises skeleton detection, skeleton transformation, mesh optimisation, and texture mapping. The presented concept enables novel and practical methods for human body 3D thermal models comparison and analysis.