cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57907/mirri/4gd5kc
title: MIRRI0075749

description: Organism type: Filamentous Fungi ; Taxon name: Exophiala mesophila ; Collection: CBS 119910 ; Country: United States of America
DOI: 10.57907/mirri/6dzodb
title: MIRRI0075996

description: Organism type: Filamentous Fungi ; Taxon name: Phaeoacremonium ; Collection: CBS 120261 ; Country: Australia
DOI: 10.57907/mirri/6sgxh3/uiccqc
title: MIRRI0075775.json

description: Strain json file
DOI: 10.57907/mirri/bpvoyj/vrvhzb
title: MIRRI0076030.json

description: Strain json file
DOI: 10.57907/mirri/cvtku2
title: MIRRI0075773

description: Organism type: Filamentous Fungi ; Taxon name: Botryosphaeria corticola ; Collection: CBS 119935 ; Country: Italy
DOI: 10.57907/mirri/d4bomv/zwxmlm
title: MIRRI0076110.json

description: Strain json file
DOI: 10.57907/mirri/eakcss
title: MIRRI0075799

description: Organism type: Filamentous Fungi ; Taxon name: Daldinia eschscholtzii ; Collection: CBS 119994 ; Country: Seychelles
DOI: 10.57907/mirri/ivi7wp/eewt2k
title: MIRRI0075797.json

description: Strain json file
DOI: 10.57907/mirri/jnpifc
title: MIRRI0075721

description: Organism type: Filamentous Fungi ; Taxon name: Fusarium aberrans ; Collection: CBS 119866 ; Country: Niger
DOI: 10.57907/mirri/odypul/kv76ve
title: MIRRI0075794.json

description: Strain json file
DOI: 10.57907/mirri/ohvsfw/8qbm6f
title: MIRRI0075915.json

description: Strain json file
DOI: 10.57907/mirri/onokaz/otjcpz
title: MIRRI0075801.json

description: Strain json file
DOI: 10.57907/mirri/ot953u/rwsfbz
title: MIRRI0076003.json

description: Strain json file
DOI: 10.57907/mirri/pda9nu/kbmyzt
title: MIRRI0075783.json

description: Strain json file
DOI: 10.57907/mirri/qhdj66
title: MIRRI0075922

description: Organism type: Filamentous Fungi ; Taxon name: Cylindrocarpon ; Collection: CBS 120173 ; Country: Slovenia
DOI: 10.57907/mirri/qyfvfj
title: MIRRI0075754

description: Organism type: Filamentous Fungi ; Taxon name: Exophiala aquamarina ; Collection: CBS 119915 ; Country: United States of America
DOI: 10.57907/mirri/rgxqnr/zrxkrz
title: MIRRI0075748.json

description: Strain json file
DOI: 10.57907/mirri/rqdfhd
title: MIRRI0075776

description: Organism type: Filamentous Fungi ; Taxon name: Diplodia sapinea ; Collection: CBS 119938 ; Country: Italy
DOI: 10.57907/mirri/tjxp38
title: MIRRI0075770

description: Organism type: Filamentous Fungi ; Taxon name: Ophiostoma penicillatum ; Collection: CBS 119932 ; Country: Austria
DOI: 10.57907/mirri/urzsxn
title: MIRRI0075959

description: Organism type: Filamentous Fungi ; Taxon name: Ophiostoma huntii ; Collection: CBS 120222
DOI: 10.57907/mirri/vrjspq/w5al7m
title: MIRRI0075999.json

description: Strain json file
DOI: 10.57907/mirri/wftl8e/bzizpa
title: MIRRI0075789.json

description: Strain json file
DOI: 10.57907/mirri/xojkqi/ea6s4x
title: MIRRI0075781.json

description: Strain json file
DOI: 10.57907/mirri/ygbwa0
title: MIRRI0075883

description: Organism type: Filamentous Fungi ; Taxon name: Didymella glomerata ; Collection: CBS 120109 ; Country: United States of America
DOI: 10.57907/mirri/ym28rl
title: MIRRI0075723

description: Organism type: Filamentous Fungi ; Taxon name: Albonectria rigidiuscula ; Collection: CBS 119868
DOI: 10.15468/dl.64mnnv
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lolium temulentum",
 "Country is Pakistan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 15 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067462-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5524/100932
title: Supporting data for "A Chromosome-scale draft genome sequence of horsegram (<i>Macrotyloma uniflorum</i>)"

description: Horsegram [<i>Macrotyloma uniflorum</i> (Lam.) Verdc.] is an underutilized warm-season diploid legume (2n=20, 22). Because of its ability to grow under water-deficient and marginal soil conditions, horsegram is a preferred choice in the era of global climate change. In recognition of its potential as a crop species, we generated and analyzed a draft genome sequence for a horsegram variety, HPK-4. Ten chromosome-scale pseudomolecules were created by aligning Illumina scaffold sequences onto a linkage map. The total length of the ten pseudomolecules was 259.2 Mb, covering 89% of the total length of the assembled sequences. A total of 36,105 genes were predicted on the assembled sequences. Diversity analysis in the 89 accessions of horsegram by dd-RAD-Seq identified 277 SNPs, suggesting narrow genetic diversity among the horsegram accessions. This is the first attempt to generate a draft genome sequence of horsegram and will provide a reference for sequence-based analysis of the horsegram germplasm.
DOI: 10.5524/100935
title: Supporting data for "Atria: An Ultra-fast and Accurate Trimmer for Adapter and Quality Trimming"

description: As Next Generation Sequencing takes a dominant role in terms of output capacity and sequence length, adapters attached to the reads and low-quality bases hinder the performance of downstream analysis directly and implicitly, such as producing false-positive single nucleotide polymorphisms (SNP), and generating fragmented assemblies. A fast trimming algorithm is in demand to remove adapters precisely, especially in read tails with relatively low quality. <br>We present a trimming program named Atria. Atria matches the adapters in paired reads and finds possible overlapped regions with a super-fast and carefully designed byte-based matching algorithm (<i>O(n)</i> time with <i>O(1)</i> space). Atria also implements multi-threading in both sequence processing and file compression and supports single-end reads. <br>Atria performs favorably in various trimming and runtime benchmarks of both simulated and real data with other cutting-edge trimmers. We also provide an ultra-fast and lightweight byte-based matching algorithm. The algorithm can be used in a broad range of short-sequence matching applications, such as primer search and seed scanning before alignment. <br>The Atria executables, source code, and benchmark scripts are available at https://github.com/cihga39871/Atria under the MIT license.
DOI: 10.5524/100942
title: Supporting data for "A high-throughput multiplexing and selection strategy to complete bacterial genomes"

description: Bacterial whole-genome sequencing, based on short-read technologies often results in a draft assembly formed by contiguous sequences. The introduction of long-read sequencing technologies permits one to unambiguously bridge those contiguous sequences into complete genomes. However, the elevated costs associated with long-read sequencing frequently limit the number of bacterial isolates that can be long-read sequenced. <br>Here we evaluated the recently released 96 barcoding kit from Oxford Nanopore Technologies (ONT) to generate complete genomes on a high-throughput basis. In addition, we propose an isolate selection strategy that optimizes a representative selection of isolates for long-read sequencing considering as input large-scale bacterial collections. <br>Despite an uneven distribution of long-reads per barcode, near-complete chromosomal sequences (assembly contiguity = 0.89) were generated for 96 <i>Escherichia coli</i> isolates with associated short-read sequencing data. The assembly contiguity of the plasmid replicons was even higher (0.98) which indicated the suitability of the multiplexing strategy for studies focused on resolving plasmid sequences. We benchmarked hybrid and ONT-only assemblies and showed that the combination of ONT sequencing data with short-read sequencing data is still highly desirable: (i) to perform an unbiased selection of isolates for long-read sequencing, (ii) to achieve an optimal genome accuracy and completeness, and (iii) to include small plasmids underrepresented in the ONT library. <br>The proposed long-read isolate selection ensures the completion of bacterial genomes that span the genome diversity inherent in large collections of bacterial isolates. We show the potential of using this multiplexing approach to close bacterial genomes on a high-throughput basis.
DOI: 10.5524/100945
title: Supporting data for "Myth-busting the provider-user relationship for digital sequence information"

description: The United Nations Convention on Biological Diversity (CBD) formally recognized the sovereign rights of nations over their biological diversity. Implicit within the treaty is the idea that mega-biodiverse countries will provide genetic resources and grant access to them and scientists in high-income countries will use these resources and share back benefits. However, little research has been conducted on how this framework is reflected in real-life scientific practice. Currently, parties to the CBD are debating whether digital sequence information (DSI) should be regulated under a new benefit-sharing framework. At this critical time point in the upcoming international negotiations, we test the fundamental hypothesis of provision and use by looking at the global patterns of access and use in scientific publications. Our data reject the provider-user relationship and suggest far more complex information flow for digital sequence information. Therefore, any new policy decisions on digital sequence information should be aware of the high level of use of DSI across low- and middle-income countries and seek to preserve open access to this crucial common good.
DOI: 10.5524/100947
title: Supporting data for "Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature"

description: Linking nucleotide sequence data (NSD) to scientific publication citations can enhance understanding of NSDs provenance, scientific use, and reuse in the community. By connecting publications with NSD records, NSD geographical provenance information, and author geographical information, it becomes possible to assess the contribution of NSD to infer trends in scientific knowledge gain at the global level.<br>We extracted and linked records from the European Nucleotide Archive to citations in open-access publications aggregated at Europe PubMed Central for this data note. A total of 8,464,292 ENA accessions with geographical provenance information were associated with publications. We conducted a data quality review to uncover potential issues in publication citation information extraction and author affiliation tagging and developed and implemented best-practice recommendations for citation extraction. We constructed flat data tables and a data warehouse with an interactive web application to enable ad hoc exploration of NSD use and summary statistics. <br>The extraction and linking of NSD with associated publication citations enables transparency. The quality review contributes to enhanced text mining methods for identifier extraction and use. Furthermore, the global provision and use of NSD enable scientists worldwide to join literature and sequence databases in a multidimensional fashion. As a concrete use case, we visualized statistics of country clusters concerning NSD access in the context of discussions around digital sequence information under the United Nations Convention on Biological Diversity.
DOI: 10.6084/m9.figshare.14705979
title: Unicycler assemblies

description: Unicycler assemblies (normal mode, version 0.4.7) using ONT and Illumina HiSeq reads. <br>ONT reads were demultiplexed and basecalled using Guppy (version 4.2.3). Porechop (version 0.2.4) was considered to trim and remove ONT adapters with default parameters. Filtlong (version 0.2.0) was used to filter the ONT reads considering a minimum length of 1 kbp (--min_length 1000), a quality phred score of 20 (--mean_q_weight 20), retaining 90% of the total number of ONT reads ( --keep_percent 90) from a maximum 40x coverage (--target_bases).
DOI: 10.6084/m9.figshare.14706015
title: Flye assemblies (long-read only assemblies)

description: Flye (version 2.8.3-b1695) [31] was run with all the passed ONT reads (phred score &gt; 7) available per barcode (--nano-raw), specifying the option to recover plasmids (--plasmids), indicating an expected genome size of 5 Mbp (--genome-size 5m) and considering 3 polishing rounds (--iterations 3). <br>ONT reads were demultiplexed and basecalled using Guppy (version 4.2.3). <br>
DOI: 10.6084/m9.figshare.14706108
title: Medaka assemblies (Flye polished assemblies)

description: Flye assemblies were polished with Medaka (version 1.2.5) https://github.com/nanoporetech/medaka specifying the model ‘r941_min_high_g360’ and considering as input all the passed ONT reads available per barcode.
DOI: 10.6084/m9.figshare.14778333
title: ONT passed reads

description: ONT passed reads of the multiplexing run with 96 barcodes. Guppy v.4.2.3 was used with high-accuracy basecalling model, to basecall and demultiplexing ONT reads
DOI: 10.15468/dl.usxy7f
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Canadian National Mycological Herbarium",
 "Country is Croatia"
 ]
}

 The dataset includes 10 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002011-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5524/100897
title: High-quality <i>de novo</i> genome from an ethanol-preserved specimen of <i>Desoria tigrina</i>

description: Genome sequencing of all known eukaryotes on Earth promises unprecedented advances in biological sciences and in biodiversity-related applied fields such as environmental management and natural product research. Advances in long read DNA sequencing make it feasible to generate high-quality genomes for many non-genetic model species. However, long read sequencing today relies on sizable quantities of high-quality, high molecular weight (hmw) DNA which is mostly obtained from fresh tissues. This is a challenge for biodiversity genomics of most metazoan species, which are tiny and need to be preserved immediately after collection. Here we present a de novo genome from an ethanol-preserved specimen of <i>Desoria tigrina</i>. For this genome assembly, we prepared the sequencing library from hmw DNA extracted from a single specimen and using a novel Ultra-Low input protocol from Pacific Biosciences. This protocol requires a DNA input of only 5 ng, permitted by a whole genome amplification step. The assembled genome has a N50 value over 5.5 Mb and contains ~96% of BUSCO genes. Thus, this genome assembly is highly contiguous and complete. This species is devoid of the biosynthetic pathway for beta-lactam antibiotics known in several <i>Collembola</i>, confirming the tight correlation of antibiotics synthesis with the species way of life. It is now possible to generate high-quality genomes from single-specimens of minute, field-preserved metazoans, exceeding the minimum contig N50 (1Mb) required by the Earth BioGenome Project.
DOI: 10.5281/zenodo.5083311
title: RNAProt: An efficient and feature-rich RNA binding protein binding site predictor

description: RNAProt Supplementary Data Archive, containing benchmark and training datasets (see content.txt for more details on included datasets)
DOI: 10.5524/100885
title: Genomic data for the montane vole (Microtus montanus)

description: Voles of the genus <i>Microtus</i> are important research organisms, yet genomic resources in the genus are lacking. Providing such resources would benefit future studies of immunology, phylogeography, cryptic diversity, and more. We sequenced and assembled nuclear genomes from two subspecies of water vole (<i>Microtus richardsoni</i>) and from the montane vole (<i>Microtus montanus</i>). <br>The montane vole is native to the western United States and Canada. Fifteen subspecies of <i>Microtus montanus</i> can be found across a range of elevations and habitats, including grasslands, alpine meadows, near stream beds, and close to agricultural land. <br><i>Microtus montanus</i> sequencing produced over 100M reads and 13x coverage. Preliminary genome assembly resulted in ~13K scaffolds with an N50 of ~3.1Mb, 8.8% Ns, and a BUSCO score of 82.6%. In addition to the nuclear assembly, mitochondrial genome assembly was also performed.
DOI: 10.5524/100888
title: Supporting data for "Fluorescence Microscopy Datasets for Training Deep Neural Networks"

description: Fluorescence microscopy is an important technique in many areas of biological research. Two factors which limit the usefulness and performance of fluorescence microscopy are photobleaching of fluorescent probes during imaging, and, when imaging live cells, phototoxicity caused by light exposure. Recently developed methods in machine learning are able to greatly improve the signal to noise ratio of acquired images. This allows researchers to record images with much shorter exposure times, which in turn minimizes photobleaching and phototoxicity by reducing the dose of light reaching the sample. To employ deep learning methods, a large amount of data is needed to train the underlying convolutional neural network. One way to do this involves use of pairs of fluorescence microscopy images acquired with long and short exposure times. We provide high quality datasets which can be used to train and evaluate deep learning methods under development. The availability of high quality data is vital for training convolutional neural networks which are used in current machine learning approaches.
DOI: 10.5524/100892
title: Supporting data for "The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity"

description: Venoms are deadly weapons to subdue prey or deter predators that have evolved independently in many animal lineages. The genomes of venomous animals are essential to understand the evolutionary mechanisms involved in the origin and diversification of venoms.<br>Here, we report the chromosome-level genome of the venomous Mediterranean cone snail, <i>Lautoconus ventricosus</i> (Caenogastropoda: Conidae). The total size of the assembly is 3.59 Gb; it has high contiguity (N50= 93.53 Mb) and 86.6 % of the genome assembled into the 35 largest scaffolds or pseudochromosomes. Based on venom gland transcriptomes, we annotated 262 complete genes encoding conotoxin precursors, hormones, and other venom-related proteins. These genes were scattered in the different pseudochromosomes and located within repetitive regions. The genes encoding conotoxin precursors were normally structured into three exons, which did not necessarily coincide with the three structural domains of the corresponding proteins. Additionally, we found evidence in the <i>L. ventricosus</i> genome for a past whole genome duplication event by means of conserved gene synteny with the <i>Pomacea canaliculata</i> genome, the only one available at the chromosome level within Caenogastropoda. The whole genome duplication event was further confirmed by the presence of a duplicated hox gene cluster. Key genes for gastropod biology including those encoding proteins related with development, shell formation, and sex were located in the genome.<br>The new high-quality <i>L. ventricosus</i> genome should become a reference for assembling and analyzing new gastropod genomes and will contribute to future evolutionary genomic studies among venomous animals.
DOI: 10.5524/100893
title: Supporting data for "SCIGA: A software for large-scale, single-cell immunoglobulin repertories analysis"

description: 10X single-cell V(D)J sequencing enables the determining of B cell immunoglobulin repertoires with paired heavy- and light- chain. Precisely and quickly analyzing 10X single-cell immunoglobulin repertoires remains a challenge, due to the high diversity of immunoglobulin repertoires and the lack of specialized software that can analyze such diverse data. In this study, the SCIGA, a specialized software for 10X single-cell immunoglobulin repertoires analysis, was developed. SCIGA is an easy-to-use pipeline that performs reads trimming, immunoglobulin sequence assembling and annotating, heavy- and light- chain pairing, statistical analysis, visualization and integrating multiple samples, all by using one line command. SCIGA was then used to profile the single-cell immunoglobulin repertoires of nine coronavirus disease 2019 (COVID-19) patients. From these repertoires, four neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified. The single-cell V(D)J sequencing data used in our study is a part of another project. <br> All raw data has been reported to the Ministry of Science and Technology of People's Republic of China, the record-filing number is 2021BAT3238.
DOI: 10.5524/100896
title: Supporting data for "StoatyDive: Evaluation and Classification of Peak Profiles for Sequencing Data"

description: The prediction of binding sites (peak-calling) is a common task in the data analysis of methods such as crosslinking immunoprecipitation in combination with high-throughput sequencing (CLIP-Seq). The predicted binding sites are often further analyzed to predict sequence motifs or structure patterns. When looking at a typical result of such high-throughput experiments, the obtained peak profiles differ largely on a genomic level. Thus, a tool is missing that evaluates and classifies the predicted peaks based on their shapes. We hereby present StoatyDive, a tool that can be used to filter for specific peak profile shapes of sequencing data such as CLIP.<br> With StoatyDive we are able to classify peak profile shapes from CLIP-seq data of the histone stem-loop-binding protein (SLBP). We compare the results to existing tools and show that StoatyDive finds more distinct peak shape clusters for CLIP data. Furthermore, we present StoatyDives capabilities as a quality control tool and as a filter to pick different shapes based on biological or technical questions for other CLIP data from different RNA binding proteins with different biological functions and numbers of RNA recognition motifs. We finally show that proteins involved in splicing, such as RBM22 and U2AF1, have potentially sharper-shaped peaks than other RNA binding proteins.<br> StoatyDive finally fills the demand for a peak shape clustering tool for CLIP-Seq data that fine-tunes downstream analysis steps such as structure or sequence motif predictions and that acts as a quality control.
DOI: 10.5524/100905
title: Supporting data for "DAPT: A package enabling Distributed Automated Parameter Testing"

description: Modern agent-based models (ABM) and other simulation models require evaluation and testing of many different parameters. Managing that testing for large scale parameter sweeps (grid searches) as well as storing simulation data requires multiple, potentially customizable steps that may vary across simulations. Furthermore, parameter testing, processing, and analysis are slowed if simulation and processing jobs cannot be shared across teammates or computational resources. While high-performance computing (HPC) has become increasingly available, models can often be tested faster through the use of multiple computers and HPC resources. To address these issues, we created the Distributed Automated Parameter Testing (DAPT) Python package. By hosting parameters in an online (and often free) "database", multiple individuals can run parameter sets simultaneously in a distributed fashion, enabling ad hoc crowdsourcing of computational power. Combining this with a flexible, scriptable tool set, teams can evaluate models and assess their underlying hypotheses quickly. Here we describe DAPT and provide an example demonstrating its use.