cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100623
title: Supporting data for "Comparison of single nucleotide variants identified by Illumina and Oxford Nanopore technologies in the context of a potential outbreak of Shiga Toxin Producing Escherichia coli"

description: We aimed to compare Illumina and Oxford Nanopore Technology (ONT) sequencing data from the two isolates of STEC O157:H7 to determine whether concordant single nucleotide variants were identified and whether inference of relatedness was consistent with the two technologies. <br> For the Illumina workflow, the time from DNA extraction to availability of results, was approximately 40 hours in comparison to the ONT workflow where serotyping, Shiga toxin subtyping variant identification were available within seven hours. After optimisation of the ONT variant filtering, on average 95% of the discrepant positions between the technologies were accounted for by methylated positions found in the described 5-Methylcytosine motif sequences, CC(A/T)GG. Of the few discrepant variants (6 and 7 difference for the two isolates) identified by the two technologies, it is likely that both methodologies contain false calls. <br> Despite these discrepancies, Illumina and ONT sequences from the same case were placed on the same phylogenetic location against a dense reference database of STEC O157:H7 genomes sequenced using the Illumina workflow. Robust SNP typing using MinION-based variant calling is possible and we provide evidence that the two technologies can be used interchangeably to type STEC O157:H7 in a public health setting.
DOI: 10.5524/100624
title: Supporting data for "Chromosomal-level assembly of the mustache toad genome using third-generation DNA sequencing and Hi-C analysis"

description: The mustache toad, Vibrissaphora ailaonica, is an endemic species to China belonging to the Megophryidae family. Like other mustache toad species, V. ailaonica males temporarily develop keratinized nuptial spines on their upper jaw during each breeding season that fall off when the breeding season ends, which probably reversed the sexual size dimorphism with males being larger than females. To investigate the genetic mechanism of the repeatedly developed keratinized spines, a high-quality reference genome of mustache toad would be a valuable resource. For genome construction, we generated 225 Gb of short reads and 277 Gb of long reads using Illumina and Pacific Biosciences (PacBio) sequencing, respectively. The sequencing data were assembled into a 3.53 Gb genome assembly with a contig N50 length of 821 Kb. Additionally, we applied Hi-C technology to identify contacts among contigs, then assembled contigs into scaffolds and identified a genome assembly with 13 chromosomes and a scaffold N50 length of 412.42 Mb. Based on the 26,227 protein-coding genes annotated in the genome, we analyzed the phylogenetic relationships of the mustache toad with other chordate species. Results showed that the mustache toad has a relatively higher evolutionary rate and separated from the marine toad, bull frog, and Tibetan frog ancestor 206.1 million years ago. Furthermore, we identified 201 expanded gene families in the mustache toad, which were mainly enriched in immune pathway, keratin filament, and metabolic processes. Using Illumina, PacBio, and Hi-C technologies, we constructed the first high-quality chromosomal-level mustache toad genome. This work not only offers a valuable reference genome for functional studies of mustache toad traits, but also provides important chromosome information for wider genome comparisons.
DOI: 10.5524/100627
title: Data supporting the 1000 plant (1KP) transcriptomes initiative

description: The 1000 Plants (1KP) transcriptomes initiative explored the genetic diversity of green plants (Viridiplantae) by sequencing RNA from 1,342 samples representing 1,173 species. All of the analyses done for the 1KP capstone, and previous studies on subsets of these data, are based on a series of de novo transcriptome assemblies and related outputs that will be described in the accompanying GigaScience publication. We also describe assessments of the data quality and an analysis to remove cross-contamination between the samples. These data will be useful to researchers with interests in specific gene families, either across the green plant tree of life or in more focused lineages.
DOI: 10.5524/100643
title: Supporting data for "Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)"

description: Castanea mollissima is widely cultivated in China for nut production. This plant also plays an important ecological role in afforestation and ecosystem services. To facilitate and expand the utilization of C. mollissima for breeding and its genetic improvement, we report here the whole genome sequence of C. mollissima. We produced a high-quality assembly of the C. mollissima genome using PacBio single-molecule sequencing. The final draft genome is approximately 785.53 Mb long, with a contig N50 size of 944 kb, and we further annotated 36,479 protein-coding genes in the genome. Phylogenetic analysis showed that C. mollissima diverged from Quercus robur, a member of the Fagaceae family, approximately 13.62 million years ago. The high-quality whole genome assembly of C. mollissima will be a valuable resource for further genetic improvement and breeding for disease resistance and nut quality.
DOI: 10.5524/100646
title: Supporting data for "A draft genome assembly of halophyte Suaeda aralocaspica, a plant that performs C4 photosynthesis within individual cells"

description: The halophyte <i>Suaeda aralocaspica</i> performs complete C<sub>4</sub> photosynthesis within individual cells (SCC<sub>4</sub>), which is distinct from typical C<sub>4</sub> plants that require the collaboration of two types of photosynthetic cells. However, despite SCC<sub>4</sub> plants having features that are valuable in engineering higher photosynthetic efficiencies in C<sub>3</sub> species, including rice, there are no reported sequenced SCC<sub>4</sub> plant genomes, which limits our understanding of the mechanisms involved in, and evolution of, SCC<sub>4</sub> photosynthesis. <br>Using Illumina and Pacbio platforms, we generated 202 Gb of clean genomic DNA sequences having a 433-fold coverage based on the 467 Mb estimated genome size of <i>S. aralocaspica</i>. The final genome assembly was 452 Mb, consisting of 4,033 scaffolds, with a scaffold N50 length of 1.83 Mb. We annotated 29,604 proteincoding genes using Evidence Modeler based on the gene information from <i>ab initio</i> predictions, homology levels with known genes, and RNA sequencing-based transcriptome evidence. We also annotated noncoding genes, including 1,651 long noncoding RNAs, 21 microRNAs, 382 transfer RNAs, 88 small nuclear RNAs, and 325 ribosomal RNAs. A complete (circular with no gaps) chloroplast genome of <i>S. aralocaspica</i> was also assembled to be 146,654 bp in length. <br>We have presented the genome sequence of<i>S. aralocaspica</i>, a SCC<sub>4</sub> plant. Knowledge of the genome of <i>S. aralocaspica</i> should increase our understanding of SCC<sub>4</sub> photosynthesis evolution and contribute to the engineering of C<sub>4</sub> photosynthesis into economically important C<sub>3</sub> crops.
DOI: 10.5524/100647
title: Supporting data for "A chromosomal-level genome assembly for the giant African snail Achatina fulica"

description: <i>Achatina fulica (A. fulica</i>), also called the giant African snail, is the largest species in the reported terrestrial mollusks. Due to its voracious appetite, wide environmental adaptability, high growth rate and reproductive capacity, the species caused a worldwide invasion, mainly in Southeast Asia, Japan, the western Pacific islands and China. <i>A. fulica</i> is a pest that is able to damage agricultural crops, as well as an intermediate host of many parasites that can threaten human health. However, genomic information of <i>A. fulica</i> is still limited, hindering genetic and genomic studies with the aim to invasion control and management of the species. Using Kmer-based method, we estimated the <i>A. fulica</i> genome size to be 2.12 Gb with a high repeat content up to 71%. About 101.6 Gb genomic long-read data of <i>A. fulica</i> were generated from the PacBio sequencing platform and assembled to the first <i>A. fulica</i> genome of 1.85 Gb with a contig N50 length of 726 kb. Using contact information from the Hi-C sequencing data, we successfully anchored 99.32% contig sequences into 31 chromosomes, leading to the final contig and scaffold N50 length of 721 kb and 59.6 Mb, respectively. The continuity, complet ness and accuracy were evaluated by genome comparison with other mollusk genomes, BUSCO assessment and genomic read mapping. 23,726 protein-coding genes were predicted from the assembled genome, among which 96.34% of the genes were functionally annotated. The phylogenetic analysis using whole genome protein-coding genes revealed that<i>A. fulica</i> separated from the common ancestor with Biomphalaria glabrata around 182 million years ago.<br> As our best knowledge, the <i>A. fulica</i> genome was the first terrestrial mollusk genome reported so far. The chromosome sequences of <i>A. fulica</i> will provide the research community a valuable resource for the population genetics and environmental adaptation studies for the species, and furthermore, for the chromosome level of evolution investigation within mollusks
DOI: 10.5524/100654
title: Supporting data for "Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information"

description: Long DNA reads produced by single molecule and pore-based sequencers are more suitable for assembly and structural variation discovery than short read DNA fragments. For de novo assembly, PacBio and Oxford Nanopore Technologies (ONT) are favorite options. However, PacBios SMRT sequencing is expensive for a full human genome assembly and costs over 40,000 USD for 30x coverage as of 2019. ONT PromethION sequencing, on the other hand, is one-twelfth the price of PacBio for the same coverage. This study aimed to compare the cost-effectiveness of ONT PromethION and PacBios SMRT sequencing in relation to the quality. Findings We performed whole genome de novo assemblies and comparison to construct an improved version of KOREF, the Korean reference genome, using sequencing data produced by PromethION and PacBio. With PromethION, an assembly using sequenced reads with 64x coverage (193 Gb, 3 flowcell sequencing) resulted in 3,725 contigs with N50s of 16.7 Mbp and a total genome length of 2.8 Gbp. It was comparable to a KOREF assembly constructed using PacBio at 62x coverage (188 Gbp, 2,695 contigs and N50s of 17.9 Mbp). When we applied Hi-C-derived long-range mapping data, an even higher quality assembly for the 64x coverage was achieved, resulting in 3,179 scaffolds with an N50 of 56.4 Mbp. Conclusion The pore-based PromethION approach provides a good quality chromosome-scale human genome assembly at a low cost with long maximum contig and scaffold lengths and is more cost-effective than PacBio at comparable quality measurements.
DOI: 10.5524/100661
title: Fish10K Pilot Project Data

description: With more than 30,000 species, fish are the largest and most ancient vertebrate group. Despite their critical roles in many ecosystems and human society, fish genomics lags behind work on birds and mammals. This severely limits our understanding of evolution and hinders progress on the conservation and sustainable use of fish. Here, we announce the Fish10K project, an international collaborative effort aiming to sequence 10,000 representative fish genomes in a systematic manner within ten years, and officially welcome collaborators to join this effort. As a step towards this goal, we herein describe the best practices for the procurement and storage of biospecimens, sequencing, and assembly strategies. To illustrate, we present the genomes of ten fish species from a cohort of 105 species chosen for technology development.
DOI: 10.17632/6wtpgr3kbj.1
title: CWL run of Alignment Workflow (CWLProv 0.6.0 Research Object)

description: The CWL alignment workflow included in this case study is designed by Data Biosphere. It adapts the alignment pipeline originally developed at Abecasis Lab, The University of Michigan. This workflow is part of NIH Data Commons initiative and comprises of four stages. First step, "Pre-align'' accepts a Compressed Alignment Map (CRAM) file (a compressed format for BAM files developed by European Bioinformatics Institute (EBI)) and human genome reference sequence as input and using underlying software utilities of SAMtools such as view, sort and fixmate returns a list of fastq files which can be used as input for the next step. The next step "Align'' also accepts the human reference genome as input along with the output files from "Pre-align'' and uses BWA-mem to generate aligned reads as BAM files. SAMBLASTER is used to mark duplicate reads and SAMtools view to convert read files from SAM to BAM format. The BAM files generated after "Align'' are sorted with "SAMtool sort''. Finally, these sorted alignment files are merged to produce single sorted BAM file using SAMtools merge in "Post-align'' step. This dataset folder is a CWLProv Research Object that captures the Common Workflow Language execution provenance, see https://w3id.org/cwl/prov/0.6.0 or use https://pypi.org/project/cwlprov/ to explore
DOI: 10.17632/97hj93mkfd.3
title: CWL run of Somatic Variant Calling Workflow (CWLProv 0.5.0 Research Object)

description: The somatic variant calling workflow included in this case study is designed by Blue Collar Bioinformatics (bcbio), a community-driven initiative to develop best-practice pipelines for variant calling, RNA-seq and small RNA analysis workflows. According to the documentation, the goal of this project is to facilitate the automated analysis of high throughput data by making the resources quantifiable, analyzable, scalable, accessible and reproducible. All the underlying tools are containerized facilitating software use in the workflow. The somatic variant calling workflow defined in CWL is available on GitHub and equipped with a well defined test dataset. This dataset folder is a CWLProv Research Object that captures the Common Workflow Language execution provenance, see https://w3id.org/cwl/prov/0.5.0 or use https://pypi.org/project/cwlprov/ to explore
DOI: 10.17632/xnwncxpw42.1
title: CWL run of RNA-seq Analysis Workflow (CWLProv 0.5.0 Research Object)

description: This workflow adapts the approach and parameter settings of Trans-Omics for precision Medicine (TOPMed). The RNA-seq pipeline originated from the Broad Institute. There are in total five steps in the workflow starting from: 1. Read alignment using STAR which produces aligned BAM files including the Genome BAM and Transcriptome BAM. 2. The Genome BAM file is processed using Picard MarkDuplicates producing an updated BAM file containing information on duplicate reads (such reads can indicate biased interpretation). 3. SAMtools index is then employed to generate an index for the BAM file, in preparation for the next step. 4. The indexed BAM file is processed further with RNA-SeQC which takes the BAM file, human genome reference sequence and Gene Transfer Format (GTF) file as inputs to generate transcriptome-level expression quantifications and standard quality control metrics. 5. In parallel with transcript quantification, isoform expression levels are quantified by RSEM. This step depends only on the output of the STAR tool, and additional RSEM reference sequences. For testing and analysis, the workflow author provided example data created by down-sampling the read files of a TOPMed public access data. Chromosome 12 was extracted from the Homo Sapien Assembly 38 reference sequence and provided by the workflow authors. The required GTF and RSEM reference data files are also provided. The workflow is well-documented with a detailed set of instructions of the steps performed to down-sample the data are also provided for transparency. The availability of example input data, use of containerization for underlying software and detailed documentation are important factors in choosing this specific CWL workflow for CWLProv evaluation. This dataset folder is a CWLProv Research Object that captures the Common Workflow Language execution provenance, see https://w3id.org/cwl/prov/0.5.0 or use https://pypi.org/project/cwl
DOI: 10.5524/100618
title: Supporting data for "CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language"

description: Massive growth in the amount of research data and computational analysis has led to increased utilization of pipeline managers in biomedical computational research. However, each of more than 100 such managers uses its own way to describe pipelines, leading to difficulty porting workflows to different environments and therefore poor reproducibility of computational studies. For this reason, the Common Workflow Language (CWL) was recently introduced as a specification for platform-independent workflow description, and work began to transition existing pipelines and workflow managers to CWL. Here, we present CWL-Airflow, an extension for the Apache Airflow pipeline manager supporting CWL. CWL-Airflow utilizes CWL v1.0 specification and can be used to run workflows on standalone MacOS/Linux servers, on clusters, or on variety cloud platforms. A sample CWL pipeline for processing of ChIP-Seq data is provided. CWL-Airflow will provide users with the features of a fully-fledged pipeline manager and an ability to execute CWL workflows anywhere Airflow can runfrom a laptop to cluster or cloud environment.
DOI: 10.5524/100621
title: Supporting data for "PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping"

description: Mapping biomedical data to functional knowledge is an essential task in bioinformatics and can be achieved by querying identifiers, e.g. gene sets, in pathway knowledgebases. However, the isoform and post-translational modification states of proteins are lost when converting input and pathways into gene-centric lists.<br>Based on the Reactome knowledgebase, we built a network of protein-protein interactions accounting for the documented isoform and modification statuses of proteins. We then implemented a command line application called PathwayMatcher (github.com/PathwayAnalysisPlatform/PathwayMatcher) to query this network. PathwayMatcher supports multiple types of omics data as input, and outputs the possibly affected biochemical reactions, subnetworks, and pathways.<br>PathwayMatcher enables refining the network-representation of pathways by including proteoforms defined as protein isoforms with post-translational modifications. The specificity of pathway analyses is hence adapted to different levels of granularity and it becomes possible to distinguish interactions between different forms of the same protein.
DOI: 10.5524/100625
title: Supporting data for "Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv"

description: The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research. Computationally driven data-intensive experiments using workflows enable Automation, Scaling, Adaption and Provenance support (ASAP). However, there are still several challenges associated with the effective sharing, publication and reproducibility of such workflows due to the incomplete capture of provenance and lack of interoperability between different technical (software) platforms. Based on best practice recommendations identified from literature on workflow design, sharing and publishing, we define a hierarchical provenance framework to achieve uniformity in the provenance and support comprehensive and fully re-executable workflows equipped with domain-specific information. To realise this framework, we present CWLProv, a standard-based format to represent any workflow-based computational analysis to produce workflow output artefacts that satisfy the various levels of provenance. We utilise open source community-driven standards; interoperable workflow definitions in Common Workflow Language (CWL), structured provenance representation using the W3C PROV model, and resource aggregation and sharing as workflow-centric Research Objects (RO) generated along with the final outputs of a given workflow enactment. We demonstrate the utility of this approach through a practical implementation of CWLProv and evaluation using real-life genomic workflows developed by independent groups. The underlying principles of the standards utilised by CWLProv enable semantically-rich and executable Research Objects that capture computational workflows with retrospective provenance such that any platform supporting CWL will be able to understand the analysis, re-use the methods for partial re-runs, or reproduce the analysis to validate the published findings.
DOI: 10.5524/100649
title: High-coverage genomes of all extant penguin taxa

description: Penguins (Sphenisciformes) are a highly diverse order of seabirds distributed widely across the Southern Hemisphere. They shared a common ancestor with Procellariiformes about 60 million years ago, and have subsequently transited from flying seabirds to flightless marine divers. Approximately 20 extant penguin species are recognized across six well-defined genera, ranging from the Galapagos Islands on the equator, to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea-ice around Antarctica. To inhabit such diverse and extreme environments, this speciose order has evolved many physiological and morphological adaptations. However, penguins are also highly sensitive to climate change, and most species are already declining or are predicted to decline under future climate change scenarios. Therefore, penguins are an exciting system for understanding the evolutionary processes of speciation, adaptation and demography. Genomic data are an emerging resource for addressing questions about such processes. Here we present 19 new high-coverage genomes that, together with two previously published genomes also available in GigaDB, encompass all extant penguin species. As such, this dataset provides a novel resource for understanding the evolutionary history within penguins, and between penguins and other avifauna. We believe that our dataset and project will be important for cultural heritage and the conservation of this iconic Southern Hemisphere species assemblage. Comparative and evolutionary genomic analyses are currently being carried out, and the consortium welcomes new members interested in contributing to this work. While this work is still underway we have published these 19 penguin genomes to provide early-release, while requesting researchers intending to use this data for similar cross-species comparisons to continue to follow the Fort Lauderdale and Toronto rules.