cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100085
title: Genomic data of the green sea turtle (<em>Chelonia mydas</em>).

description: Green turtles are long-lived and may take up to 59 years to reach sexual maturity. Undertaking tremendous feats of navigation, adults return to the same beach to breed each season.<br> DNA from the green sea turtle was collected in Hong Kong. We sequenced the 2.24 Gb genome to a depth of approximately 82.3 X with short reads from a series of libraries with various insert sizes ( 170bp, 500bp, 800bp, 2kb, 5kb, 10kb,20kb and 40kb) on a HiSeq 2000 sequencer.<br>The assembled scaffolds of high quality sequences total 180.94 Gb, with the contig and scaffold N50 values of 20.4 kb and 3.78 Mb respectively. We identified 19,633 protein-coding genes with an mean length of 1456 bp.Experimental procedures and animal care were conducted in strict accordance with guidelines approved by the RIKEN Animal Experiments Committee (Approval IDs H14-23 and H16-10).
DOI: 10.5524/100086
title: Genomic data of the soft shell turtle (<em>Pelodiscus sinensis</em>).

description: The soft shell turtle can reach a carapace length of 1 ft (0.30 m). It has webbed feet for swimming. They are called "softshell" because their carapace lacks horny scutes (scales). The carapace is leathery and pliable, particularly at the sides. It is commercially farmed in vast numbers for the food trade. <br> DNA from the soft shell turtle was collected in Japan. We sequenced the 2.21 Gb genome to a depth of approximately 105.6 X with short reads from a series of libraries with various insert sizes ( 170bp, 500bp, 800bp, 2kb, 5kb, 10kb,20kb and 40kb) on a HiSeq 2000 sequencer.<br>The assembled scaffolds of high quality sequences total 221.7 Gb, with the contig and scaffold N50 values of 21.9 kb and 3.33 Mb respectively. We identified 19,327 protein-coding genes with an mean length of ~1500bp. Experimental procedures and animal care were conducted in strict accordance with guidelines approved by the RIKEN Animal Experiments Committee (Approval IDs H14-23 and H16-10).
DOI: 10.5524/100090
title: Supporting materials from "Think globally and solve locally: secondary memory-based network learning for automated multi-species function prediction".

description: In the GigaScience manuscript associated with this data the authors propose a novel framework for scalable network-based learning of multi-species automated protein function prediction (AFP) based on both a novel algorthmic approach and the adoption of innovative technologies.
The work focuses on the processing of big networks for multi-species AFP using single off-the-shelf computers, a very difficult and in most case unfeasible task, due to the main memory limitations of ordinary computers.
The proposed algorithmic vertex-centric approach solves locally the AFP problem, by processing iteratively only small parts of the overall network, while still exploiting the global topology of the network.
The computation is based on novel secondary memory-based technologies to overcome the main memory limitation of ordinary off-the-shelf computers.
As an example, to show the feasibility and effectiveness of the proposed approach, 2 networks were constructed and analyzed. The results are contained here.
DOI: 10.5524/100092
title: MicroCT scans of freshly fixed and museum earthworm specimens.

description: <br>
Micro-computed tomography (µCT), a digital X-ray-based imaging technique, has developed into an important tool for the study of animal morphology. Although molecular tools are increasingly employed to decipher invertebrate systematics, earthworm (<em>Annelida: Clitellata: 'Oligochaeta'</em>) taxonomy is still largely based on conventional dissection, resulting in data that are mostly unsuitable for dissemination through online databases. In order to evaluate if µCT in combination with soft tissue staining techniques could be used to expand the existing set of tools available for studying internal and external structures of earthworms, µCT scans of freshly fixed and museum specimens were collected.<br>
Scout images revealed full penetration of tissues by the staining agent. The attained isotropic voxel resolutions permit identification of internal and external structures conventionally used in earthworm taxonomy. The projection as well as the reconstruction images are archived here and are publicly available for download.<br>
The dataset presented shows that earthworms constitute suitable candidates for CT scanning in combination with soft tissue staining. Not only are the data comparable to results derived from traditional dissection techniques, but they also permit interactively exploring earthworm morphology and anatomy. The approach pursued here can be applied to freshly fixed as well as museum specimens, which is of particular importance when considering the use of rare or valuable museum material.<br>
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DOI: 10.5524/100094
title: Data and software to accompany the paper: Applying compressed sensing to genome-wide association studies.

description: The aim of a genome-wide association study (GWAS) is to isolate DNA markers for variants affecting phenotypes of interest. Linear regression is employed for this purpose, and in recent years a signal-processing paradigm known as compressed sensing (CS) has coalesced around a particular class of regression techniques. CS is not a method in its own right, but rather a body of theory regarding signal recovery when the number of predictor variables (i.e., genotyped markers) exceeds the sample size. The paper shows the applicability of compressed sensing (CS) theory to genome-wide association studies (GWAS), where the purpose is to nd trait-associated tagging markers (genetic variants). Analysis scripts are contained in the compressed CS file. Mock data and scripts are found in the compressed GD file. The example scripts found in the CS repository require the GD files to be unpacked in a separate folder. Please look at accompanying readme pdfs for both repositories and annotations in the example scripts before using.
DOI: 10.5524/100096
title: Supporting material for: De novo assembly of a haplotype-resolved human genome.

description: Here we provide the first de novo haplotype-resolved diploid genome sequence of an Asian individual using a unique de novo assembly pipeline. Our pipeline uses fosmid pooling and whole genome shotgun strategies, based on next generation sequencing (NGS) technology. The assembled genome contains 5.15 Gb, with a haplotype N50 of 484 kb. This haplotype-resolved genome represents the most complete genome assembly so far. Our analysis further identified previously undetected indels and novel coding sequences, and thus provides the most complete representation of an individuals genetic variation. <br> We generated ~614,850 fosmid clones ranging from 20 kb-80 kb with a mean of 36kb, approximately 30 fosmid clones were pooled and each pool had one or two DNA libraries sequenced using Hiseq 2000. In total, 1,712 Gb of raw sequence data was generated for all the pooled fosmid libraries. Please see the linked paper for assembly pipeline details. We then analysed the newly generated haploid-resolved diploid genome (HDG) for SNPs, INDELs, inversions and translocations, of which we identified 3,580,000 SNPs, 762,000 short INDELs (&lt;50bp) and 30,000 long INDELs, 111 inversions and 168 translocations.
DOI: 10.5524/100045
title: Raw data, assembly and annotation results for: “Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification”

description: The following data comes from the study Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification, which is the first systematic meta-barcoding study sequencing the total DNA from insect communities independent of PCR amplification. Following mitochondrial enrichment using differential centrifugation, a preliminary sample and a formal sample are achieved respectively with 2.2G and 13.2G from the Illumina HiSeq 2000 platform using 100 bp paired-end (PE) sequencing, following manufacturers instructions. The data was assembled using SOAPdenovo2 and annotated using the MT_annotation_BGI pipeline (tools and pipelines available here: doi:10.5524/100046). Further details are available in the published paper and the metadata provided in the MIMS formatted table.
DOI: 10.5524/100046
title: Software and supporting material for: "Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification".

description: The software is a pipeline for mitochondrial protein annotation in mixed bulk samples. The pipeline annotates mitochondrial genes using homolog prediction with TBLASTN based on known complete mitochondrial genomes from GenBank RefSeq. The BLAST results were then used to determine gene ontology (e.g., mRNA and coding sequence regions) using Genewise. Annotation results include gff format annotation file, DNA and protein sequences of annotated genes. Compared to other mitochondrial annotation pipelines, the MT_annotation_BGI pipeline is easier to run a batch of annotation tasks with high speed and precision. For additional methodological details see the published paper using an example of bulk insect data suitable for running on this pipeline (see dataset here: doi:10.5524/100045).
DOI: 10.5524/100054
title: Genomic data from Aegilops tauschii - The Progenitor of Wheat D Genome

description: A spontaneous hybridization of the wild diploid grass Aegilops tauschii (2n=14, DD) with cultivated tetraploid wheat Triticum turgidum (2n=4x=28, AABB) 8,000~10,000 years ago in the Fertile Crescent resulted in the bread wheat (Triticum aestivum; 2n=6x=42, AABBDD), one of the earliest cultivated crops in modern agriculture. We sequenced the 4.36-gigabase (Gb) genome of Ae. tauschii by generating ~90x genome coverage of short reads from a series of libraries with various insert sizes. The assembled scaffolds of high quality sequences represent 83.4% of the genome, in which 65.9% comprised of repetitive elements. Assisted with comprehensive RNA-Seq data, we identified 43,150 protein-coding genes, with 30,697 (71.1%) of them uniquely anchored to chromosomes based on an integrated density genetic map. A number of agriculturally relevant gene families, such as disease resistance, abiotic stress tolerance, and grain quality genes, were found to expand in Ae. tauschii. The draft genome of Ae. tauschii hence provides novel insights into its role in enabling environmental adaptation of common wheat and in defining the large and complicated genomes of wheat species.
DOI: 10.5524/100059
title: De novo high-coverage sequencing and annotated assemblies of the budgerigar genome

description: <b>Background:</b> Parrots are considered one of the most behaviorally advanced vertebrate groups. They have an advanced ability of vocal learning. Parrots can imitate human speech, synchronize their body movements to a rhythmic beat, and understand complex concepts of referential meaning to sounds. However, very little is known about the genetics of these traits. In order to understand the molecular and genetic basis of these traits we need whole genome sequencing and a robust assembly of coding and noncoding regions of a parrot genome including regulatory regions and repetitive elements.<br><br><b>Findings:</b> Here we present a genomic resource for the budgerigar, an Australian Parakeet (<i>Melopsittacus undulatus</i>) that is the most widely used parrot species for studying vocal learning. Specifically, we present the genomic reads, four high quality annotated assemblies and optical maps. This sequence reads were in part used for the Assemblathon 2 competition (see dataset doi:10.5524/100060). The sequence data presented here includes over 300X raw read coverage from multiple sequencing technologies (454 Titanium, 454 Flexplus, Illumina and Pacific Biosciences) and chromosome optical maps from a single male animal. The reads and optical maps were used to create hybrid assemblies representing some of the largest genome scaffolds to date for a bird genome using next generation sequence technology. Annotation of these assemblies was generated using brain transcriptome sequence assemblies.<br><br><b>Conclusions:</b> Along several quality metric dimensions, these assemblies are comparable to or better than the Chicken and Zebra Finch genome assemblies that were built from traditional Sanger sequencing reads. These assemblies are sufficient to analyze difficult to sequence and assemble regions, including those not yet assembled in the finch genome, and promoter regions of genes deferentially regulated in vocal learning brain regions.<br>
DOI: 10.5524/100060
title: Assemblathon 2 assemblies.

description: Assemblathon 2 is a genome assembly contest where participating teams attempted to assemble genomes for three vertebrate species using a mixture of next-generation sequencing data. In total, 43 assemblies were submitted for three species (15 for bird, 16 for fish, and 12 for snake). These assemblies were assessed using a wide variety of statistical approaches as well as using experimental data from Fosmid sequences and optical maps.
DOI: 10.5524/100065
title: Genomic and transcriptomic data from the Brandt's bat (<em>Myotis brandtii</em>).

description: Brandt's bat (<em>Myotis brandtii</em>) is a species of vesper bat in the family Vespertilionidae. It is found throughout most of Europe and parts of Asia. It is known for its extreme longevity quotient, approximately twice that of humans.<br> A whole-genome shotgun strategy was applied to sequence the genome of an adult male Brandts bat (<em>M. brandtii</em>) from the Obvalnaya cave in Russia. We also sequenced liver, kidney and brain transcriptomes of hibernating and summer-active M. brandtii. Approximately 156 Gb (or 78 × ) genome data including 101 Gb (or 51 × ) short insert size reads were generated, resulting in a high-quality assembly with scaffold N50 of 3.1 Mb and contig N50 of 21 kb
DOI: 10.5524/100068
title: Example files and supporting material for "EMPeror: An interactive analysis and visualization tool for high throughput microbial ecology datasets."

description: EMPeror is an interactive next generation tool for the analysis, visualization and understanding of high throughput microbial ecology datasets. <br> Due to its tailor-made graphical user interface, delving into a new dataset to elucidate the patterns hidden in the data, has never been easier. EMPeror brings a rich set of customizations and modifications that can be integrated into any QIIME compliant dataset; with lightweight data files and hardware accelerated graphics, constitutes itself as the state of the art for analyzing N-dimensional data using principal coordinates analysis. <br> The data presented here is the version of the software at point of publication, together with the example results used to illiustrate the functionality in the associated GigaScience paper. In addition, we host the script used to generate the EMPeror input file to create these examples, which some users may find useful to help replicate the example.
DOI: 10.5524/100069
title: GigaGalaxy workflows and histories from “Galaxy tools to study genome diversity”

description: Intra-species genetic variation can be used to investigate population structure, selection, and gene flow in non-model vertebrates; and due to the plummeting costs for genome sequencing, it is now possible for small labs to obtain full-genome variation data from their species of interest. However, those labs may not have easy access to, and familiarity with, computational tools to analyze those data. <br>A suite of tools for the Galaxy web server have been created aimed at handling nucleotide and amino-acid polymorphisms discovered by full-genome sequencing of several individuals of the same species, or using a SNP genotyping microarray. <br>In addition to providing user-friendly tools, a main goal is to make published analyses reproducible. These tools are presented in a GigaScience publication (doi: 10.1186/2047-217X-2-17), and in order to facilitate readers to repeat and recreate the examples given in the paper, we present here the pipelines and histories, both accessible from our GigaGalaxy server, and as Galaxy XML files available to download. The five workflows included relate to examples in the paper dealing with nuclear-genome diversity in non-human vertebrates, and also illustrate the application of the tools to fungal genomes, human biomedical data, and mitochondrial sequences.
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DOI: 10.5524/100072
title: Genomic data of the Chinese tree shrew (<em>Tupaia chinensis</em>).

description: Chinese tree shrews (<em>Tupaia belangeri chinensis</em>) possess many features valuable in animals used as experimental models in biomedical research. Currently, there are numerous attempts to employ tree shrews as models for a variety of human disorders: depression, myopia, hepatitis B and C virus infections, and hepatocellular carcinoma, to name a few. Here we present a publicly available annotated genome sequence for the Chinese tree shrew. Phylogenomic analysis of the tree shrew and other mammalians highly support its close affinity to primates.<br><br> DNA form the tree shrew was collected in Yunnan, China. We sequenced the 3.2 Gb genome to a depth of approximately 79.2x with short reads from a series of libraries with various insert sizes ( 170bp, 500bp, 800bp, 2kb, 5kb, 10kb, 20kb and 40kb).<br>The assembled scaffolds of high quality sequences total 253.5 Gb, with the contig and scaffold N50 values of 22 kb and 3.65 Mb respectively. We identified 22,063 protein-coding genes. <br>Experimental procedures and animal care were conducted in strict accordance with guidelines approved by the RIKEN Animal Experiments Committee (Approval IDs H14-23 and H16-10).
DOI: 10.5524/100075
title: Genomic data from the saker falcon (<em>Falco cherrug</em>).

description: The saker falcon (<em>Falco cherrug</em>) is the national bird of Hungary, and has unique morphological, physiological and behavioural adaptations allowing them to be successful hunters. It often hunts by horizontal pursuit of rodents and birds, rather than the high-speed dives (stoop from a height) some other birds of prey such as the peregrine use. <br>Here we present the data for the saker falcon genome that was obtained using an Illumina HiSeq 2000 platform that generated a 136.21 Gb sequence. Paired-end libraries with insert sizes of 170, 500 and 800 bp (short inserts) and 5, 10 and 20 kb (long inserts) were constructed. The initial genome size was estimated at 1.2 Gb, suggesting a genome coverage of 113.51x. SOAPdenovo was used for assembly and resulted in scaffold N50 and contig values of 4.15 Mb and 31.2 kb, respectively. Fosmid-based Sanger sequencing confirmed &gt;97% coverage of euchromatic DNA. This data will help provide insights into the evolution of the sakers predatory lifestyle.
DOI: 10.5524/100077
title: Genomic data of the Chinese alligator (<em>Alligator sinensis</em>).

description: The Chinese alligator (<em>Alligator sinensis</em>), a freshwater crocodilian endemic to China, is one of the most endangered crocodilian species. Currently, there are ~100 Chinese alligators in the wild and ~10 000 captive individuals in Zhejiang and Anhui Provinces. We chose the Chinese alligator for genome sequencing with the hope of providing information that could help design scientific captive-breeding programs for population recovery project of this endangered species. <br>DNA from the chinese aligator was collected in Zhejiang Province, China. We sequenced the 2.3Gb genome with short reads from a series of libraries with various insert sizes ( 170bp, 500bp, 800bp, 2kb, 5kb, 10kb and 20kb) on a HiSeq 2000 sequencer.<br>The assembled scaffolds of high quality sequences total 314Gb, with the contig and scaffold N50 values of 23.4kb and 2.2Mb respectively. We identified 22,200 protein-coding genes with an mean length of 1403bp.
DOI: 10.5524/100079
title: Genomic data of the diploid cotton (<em>Gossypium raimondii</em>).

description: Cotton is one of the most economically important crop plants worldwide. Its fiber, commonly known as cotton lint, is the principal natural source for the textile industry.<br>We have sequenced and assembled a draft genome of <em>G. raimondii</em>, whose progenitor is the putative contributor of the D subgenome to the economically important fiber-producing cotton species Gossypium hirsutum and Gossypium barbadense. <br>We sequenced the 0.78 Gb genome to a depth of approximately 103 X with short reads from a series of libraries with various insert sizes ( 170 bp, 250 bp, 500 bp, 800 bp, 2 kb, 5 kb, 10 kb, 20 kb and 40 kb) on a HiSeq 2000 sequencer.<br>The assembled scaffolds of high quality sequences total 78.7 Gb, with the contig and scaffold N50 values of 44.9 kb and 2.3 Mb respectively. We identified 40,976 protein-coding genes with an mean length of 1104 bb.
DOI: 10.5524/100083
title: Genomic data of the pear (<em>Pyrus bretschneideri</em>).

description: Pear, the third most important temperate fruit species after grape and apple, belongs to the subfamily Pomoideae in the family Rosaceae. The majority of cultivated pears are functional diploids (2n = 34). The Pyrus genus is genetically diverse with thousands of cultivars, but it can be divided into two major groups, Occidental pears (European pears) and Oriental pears (Asiatic pears). <br>We sequenced the genome to a depth of approximately 107 X with short reads from a series of libraries with various insert sizes ( 170bp, 500bp, 800bp, 2kb, 5kb, 10kb, 20kb and 40kb) on a HiSeq 2000 sequencer.<br>The assembled scaffolds of high quality sequences total 57 Gb. We identified 42,812 protein-coding genes.
DOI: 10.5524/100084
title: Genomic data of the plum (<em>Prunus mume</em>).

description: The Plum (<em>Prunus mume</em>), was domesticated in China more than 3,000 years ago as ornamental plant and fruit, is one of the first genomes among Prunus subfamilies of Rosaceae to be sequenced.<br>DNA from the plum was collected in Tongmai town, Tibet, China. We sequenced the genome to a depth of approximately 101.4 X with short reads from a series of libraries with various insert sizes ( 180bp, 500bp, 800bp, 2kb, 5kb, 10kb, 20kb and 40kb) on a HiSeq 2000 sequencer.<br>The assembled scaffolds of high quality sequences total 28.4 Gb with the contig and scaffold N50 values of 31.8 kb and 577.8 kb respectively.
DOI: 10.5524/100087
title: Genomic data of the watermelon (<em>Citrullus lanatus</em>).

description: Watermelon (<em>Citrullus lanatus</em> is an important cucurbit crop grown throughout the world. The annual world production of watermelon is about 90 million tons, making it among the top five most consumed fresh fruits (http://faostat.fao.org/). <br>We sequenced the 0.425 Gb genome to a depth of approximately 108.6 x with short reads from a series of libraries with various insert sizes ( 100-200 bp, 400 bp, 2 kb, 5 kb, 10 kb and 20 kb) on a HiSeq 2000 sequencer.<br>The assembled scaffolds of high quality sequences total 46.18 Gb, with the contig and scaffold N50 values of 26.38 kb and 2.38 Mb respectively. We identified 23,440 protein-coding genes.