cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100290
title: Supporting data for "Hybrid de novo genome assembly of the Chinese herbal fleabane Erigeron breviscapus"

description: The plants in the Erigeron genus of the Compositae (Asteraceae) family are commonly called fleabanes, possibly due to the belief that certain chemicals in these plants repel fleas. In the traditional Chinese medicine, Erigeron breviscapus, which is native to China, was widely used in the treatment of cerebrovascular disease. A handful of bioactive compounds, including scutellarin, 3,5-dicaffeoylquinic acid, and 3,4-dicaffeoylquinic acid, have been isolated from the plant. With the purpose of finding novel medicinal compounds and understanding their biosynthetic pathways, we propose to sequence the genome of E. breviscapus.<br>
We assembled the highly heterozygous E. breviscapus genome using a combination of PacBio single-molecular real-time sequencing method and next-generation sequencing method on the Illumina HiSeq platform. The final draft genome is approximately 1.2 Gb, with the contig and scaffold N50 sizes of 18.8 kb and 31.5 kb, respectively. Further analyses predicted 37,504 protein-coding genes in the E. breviscapus genome, and 8,172 shared gene families among Compositae species.<br>
The E. breviscapus genome provides a valuable resource for the investigation of novel bioactive compounds in this Chinese herb.
DOI: 10.5524/100296
title: Supporting data for "Transcriptional mapping of the primary somatosensory cortex upon sensory deprivation"

description: Experience-dependent plasticity (EDP) is essential for anatomical and functional maturation of sensory circuits during development. Although the principal synaptic and circuit mechanisms of EDP are increasingly well studied experimentally and computationally, its molecular mechanisms remain largely elusive. EDP can be readily studied in the rodent barrel cortex, where each barrel column preferentially represents deflections of its own principal whisker. Depriving select whiskers while sparing their neighbours introduces competition between barrel columns, ultimately leading to weakening of intracortical, translaminar (i.e. Cortical Layer (L)4-to-L2/3) feed-forward excitatory projections in the deprived columns. The same synapses are potentiated in the neighbouring spared columns. These experience-dependent alterations of synaptic strength are thought to underlie somatosensory map plasticity. We used RNA sequencing in this model system to uncover cortical-column and -layer specific changes on the transcriptome level that are induced by altered sensory experience. br /
Column- and layer-specific barrel cortical tissues were collected from juvenile mice with all whiskers intact and mice that received 11-12 days long whisker (C-row) deprivation before high quality RNA was purified and sequenced. The current dataset entails an average of 50 million paired-end reads per sample, 75 base pairs in length. On average, 90.15% of reads could be uniquely mapped to the mm10 reference mouse genome.br /
DOI: 10.5524/100303
title: Supporting data for "Comparative performance of the BGISEQ-500 vs Illumina sequencing platforms for palaeogenomic sequencing"

description: Ancient DNA research has been revolutionised following development of Next Generation Sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform, on DNA extracted from eight historic and ancient dog and wolf samples.<br>
The data generated was largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (p=0.371) and average sequence length (p=0718) of endogenous nuclear DNA, sequence GC content (p=0.311), double stranded DNA damage rate (p=0.309), and sequence clonality (p=0.093). Small significant differences were found in single strand DNA damage rate (S, slight lower for the BGISEQ-500, p=0.011) and the background rate of difference from the reference genome (, slightly higher for BGISEQ-500, p=0.012). This may result from the differences in amplification cycles used to PCR amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (p=0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from three of the samples with overall very low levels of endogenous DNA. <br>
Although we acknowledge our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent valid and potentially valuable alternative platform for palaeogenomic data generation, that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.
DOI: 10.5524/100304
title: Supporting data for "Calculating quality of public high-throughput sequencing data to obtain suitable subset for reanalysis from the Sequence Read Archive"

description: It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing number of submissions of high-throughput sequencing (HTSeq) data to public repositories prevents users from choosing a suitable data set from among the large number of search results. Repository users need to be able to set a threshold to reduce the number of results to obtain a suitable subset of
high-quality data for reanalysis.<br>
We calculated the quality of sequencing data archived in a public data repository, the Sequence Read Archive (SRA), by using the quality control software FastQC. We obtained quality values for 1,171,313 experiments, which can be used to evaluate the suitability of data for reuse. We also visualized the data distribution in SRA by integrating the quality information and metadata of experiments and samples.<br>
We provide quality information of all of the archived sequencing data which enable users to obtain sufficient quality sequencing data for reanalyses. The calculated quality data are available to the public in various formats. Our data also provide an example of enhancing the reuse of public data by adding metadata to published research data by a third party.
DOI: 10.5524/100309
title: Supporting data for "A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation"

description: Wine is a complex beverage, comprising hundreds of metabolites produced through the action of yeasts and bacteria in fermenting grape must. To ensure a robust and reliable fermentation, most commercial wines are produced via inoculation with commercial strains of the major wine yeast, Saccharomyces cerevisiae. However, there is a growing trend towards the use of uninoculated or wild fermentations, in which the yeasts and bacteria that are naturally associated with the vineyard and winery perform the fermentation. In doing so, the varied metabolic contributions of the numerous non-Saccharomyces species in this microbial community are thought to impart complexity and desirable taste and aroma attributes to wild ferments in comparison to their inoculated counterparts.
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To map the microflora of spontaneous fermentation, metagenomic techniques were employed to characterize and monitor the progression of fungal species in several wild fermentations. Both amplicon-based ribosomal DNA internal transcribed spacer (ITS) phylotyping (meta-barcoding) and shotgun metagenomics were used to assess community structure. While providing a sensitive and highly accurate means of characterizing the wine microbiome, the shotgun metagenomic data also uncovered a significant over-abundance bias in the ITS phylotyping abundance estimations for the common non-Saccharomyces wine yeast genus Metschnikowia.
DOI: 10.5524/100272
title: Supporting data for "drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes"

description: Virus discovery using high-throughput next-generation sequencing (NGS) has become more commonplace. However, although analysis of deep NGS data allows us to identity potential pathogens, the entire analytical procedure requires competency in the bioinformatics domain, which includes implementing proper software packages and preparing prerequisite databases. Simple and user-friendly bioinformatics pipelines are urgently required to obtain complete viral genome sequences from metagenomic data.<br>
Here we present a pipeline, drVM (detect and reconstruct known viral genomes from metagenomes), for rapid viral read identification, genus-level read partition, read normalization, de novo assembly, sequence annotation and coverage profiling. The first two procedures and sequence annotation rely on known viral genomes as a reference database. We also present the validation results of the analysis of over 300 previously published sequencing runs, to provide complete viral genome assemblies for a variety of virus types including DNA viruses, RNA viruses and retroviruses. <br>drVM is available for free download here and is also assembled as a Docker container, an Amazon machine image and a virtual machine to facilitate seamless deployment. GigaDB is hosting the version of the software as reviewed in the associated article, please refer to the sourceforge site for the most recent updates to the software.
DOI: 10.5524/100274
title: An updated reference human genome dataset of the BGISEQ-500 sequencer

description: The BGISEQ-500 is a new desktop sequencer developed by BGI. Using DNA nanoballs (DNB) and combinational probe-anchor synthesis (cPAS) developed from Complete Genomics sequencing technology, it generates short reads at a large scale, which can help fulfill the growing demands for sequencing. Here, we present the first human whole genome sequencing dataset from the BGISEQ-500. The dataset was generated by sequencing the widely-used Genome in a Bottle Consortium cell line, HG001 (NA12878). We have previously released the paired end 50bp (PE50) sequences (DOI:10.5524/100252) and here we present the PE100 reads from same sample, together with the assembled genome. We also included examples of the raw images from the sequencer for reference. Finally, we carried out variation calling based on the dataset and compared that to similar amounts of publicly available HiSeq2500 data and the previously identified high confident variations in this previously sequenced genome.
DOI: 10.5524/100275
title: Supporting data for "RED-ML: a novel, effective RNA editing detection method based on machine learning"

description: With the advancement of second generation sequencing techniques, our ability to detect and quantify RNA editing on a global scale has been vastly improved. As a result, RNA editing is now being studied under a growing number of biological conditions so that its biochemical mechanisms and functional roles can be further understood. However, a major barrier that prevents RNA editing from being a routine RNA-seq analysis, similar to gene expression and splicing analysis for example, is the lack of user-friendly and effective computational tools.<br>
Based on years of experience of analyzing RNA editing using diverse RNA-seq datasets, we have developed a software tool RED-ML: RNA Editing Detection based on Machine learning (pronounced as red ML). The input to RED-ML can be as simple as a single BAM file, while it can also take advantage of matched genomic variant information when available. The output not only contains detected RNA editing sites, but also a confidence score to facilitate downstream filtering. We have carefully designed validation experiments and performed extensive comparison and analysis to show the efficiency and effectiveness of RED-ML under different conditions, and it can accurately detect novel RNA editing sites without relying on curated RNA editing databases. We have also made this tool freely available via GitHub.
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We have developed a highly accurate, speedy and general-purpose tool for RNA editing detection using RNA-seq data. With the availability of RED-ML, it is now possible to conveniently make RNA editing a routine analysis of RNA-seq. We believe this can greatly benefit the RNA editing research community and has profound impact to accelerate our understanding of this intriguing post-transcriptional modification process.
DOI: 10.5524/100277
title: Supporting data for "A reference gene set construction using RNA-seq of multiple tissues of Chinese Giant Salamander, Andrias davidianus"

description: Chinese giant salamander (CGS) is the largest extant amphibian species in the world. Owing to its evolutionary position and four peculiar phenomenon of life (longevity, starvation tolerance, regenerative ability, and hatch without sunshine), it is an invaluable model species for research. However, lack of genomic resources and its huge (~50 GB) difficult to assemble genome, leads to slow study progression in this field.
Here we report the sequenced transcriptome of more than twenty tissues from adult specimens using Illumina Hiseq 2000 technology, and a total of 93,366 non-redundant transcripts with a mean length of 1,326 bp. We for the first time developed an efficient pipeline to construct a high quality reference gene set of CGS and obtained 26,135 coding genes. BUSCO and homologous assessment showed that our assembly captured 70.6 % of vertebrate universal single-copy orthologs.
DOI: 10.5524/100280
title: Supporting data for "A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana"

description: The mycalesine butterfly Bicyclus anynana, the Squinting bush brown, is a model organism in the study of lepidopteran ecology, development and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species.
Eight libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology. 128 Gb raw Illumina data were filtered to 124 Gb and assembled to a final size of 475 Mb (~260X assembly coverage). Contigs were scaffolded using mate-pair, transcriptome and PacBio data into 10,800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements, and encodes a total of 22,642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. 
We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html).
DOI: 10.5524/100282
title: Supporting data for "PSSMHCpan: a novel PSSM based software for predicting class I peptide-HLA binding affinity"

description: Predicting peptides binding affinity with human leukocyte antigen (HLA) is a crucial step in developing powerful antitumor vaccine for cancer immunotherapy. Currently available methods work quite well in predicting peptide binding affinity with HLA alleles such as HLA-A*0201, HLA-A*0101, and HLA-B*0702 in terms of sensitivity and specificity. However, quite a few types of HLA alleles that are present in majority of human populations including HLA-A*0202, HLA-A*0203, HLA-A*6802, HLA-B*5101, HLA-B*5301, HLA-B*5401 and HLA-B*5701 still cannot be predicted with satisfactory accuracy using currently available methods. Further, currently most popularly used methods for predicting peptides binding affinity are inefficient in identifying neoantigens from large quantity of whole genome and transcriptome sequencing data.<br>
Here we present a Position Specific Scoring Matrix (PSSM) based software called PSSMHCpan to accurately and efficiently predict peptide binding affinity with a broad coverage of HLA class I alleles. We evaluated the performance of PSSMHCpan by analyzing 10-fold cross-validation on a training database containing 87 HLA alleles and obtained an average area under receiver operating characteristic curve (AUC) of 0.94 and accuracy ACC of 0.85. In an independent dataset (Peptide Database of Cancer Immunity) evaluation, PSSMHCpan is substantially better than popularly used NetMHC-4.0, NetMHCpan-3.0, PickPocket, Nebula, and SMM with a sensitivity of 0.90, as compared to 0.74, 0.81, 0.77, 0.24 and 0.79. In addition, PSSMHCpan is more than 197 times faster than NetMHC-4.0, NetMHCpan-3.0, PickPocket, sNebula and SMM when predicting neoantigens from 661,263 peptides from a breast tumor sample. Finally, we built a neoantigen prediction pipeline and identified 117,017 neoantigens from 467 cancer samples of various cancers from TCGA.<br>
PSSMHCpan is superior to currently available methods in predicting peptide binding affinity with a broad coverage of HLA class I alleles.
DOI: 10.5524/100283
title: Supporting data for "The need to approximate the use-case in clinical machine learning"

description: The availability of smartphone and wearable sensor technology is leading to a rapid accumulation of human subject data, and machine learning is emerging as a technique to map that data into clinical predictions. As machine learning algorithms are increasingly used to support clinical decision making, it is vital to reliably quantify their prediction accuracy. Cross-validation is the standard approach where the accuracy of such algorithms is evaluated on data the algorithm has not seen during training. However, for this procedure to be meaningful, the relationship between the training and validation set should mimic the relationship between the training set and the dataset expected for the clinical use. Here we compared two popular cross-validation methods: record-wise and subject-wise. The subject-wise procedure mirrors the clinically relevant use-case scenario of diagnosing/identifying patterns in newly recruited subjects. The record-wise strategy has no such interpretation.<br>
Using both a publicly available dataset and a simulation, we found that record-wise cross-validation often massively overestimates the prediction accuracy of the algorithms. We also conducted a systematic review of the relevant literature, and found that this overly optimistic method is used by almost half of the retrieved studies that used accelerometers, wearable sensors, or smartphones to predict clinical outcomes. <br>
As we move towards an era of machine learning based diagnosis and treatment, using proper methods to evaluate their accuracy is crucial, as results that are overly optimistic can mislead both clinicians and data scientists.
DOI: 10.5524/100284
title: Supporting data for "NanoSim: nanopore sequence read simulator based on statistical characterization"

description: The MinION sequencing instrument from Oxford Nanopore Technologies (ONT) produces long read lengths from single-molecule sequencing, a valuable feature for detailed genome characterization. To realize the potential of this platform, a number of groups are developing bioinformatics tools tuned for the unique characteristics of its data. We note that these development efforts would benefit from a simulator software, output of which could be used to benchmark analysis tools.<br>
Here, we introduce NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology. The first step of NanoSim is read characterization, which provides a comprehensive alignment-based analysis, and generates a set of read profiles serving as the input to the next step, the simulation stage. The simulation stage uses the model built in the previous step to produce in silico reads for a given reference genome. NanoSim is written in Python and R. <br>
In this work, we model the base-calling errors of ONT reads to inform the simulation of sequences with similar characteristics. We showcase the performance of NanoSim on publicly available datasets generated using the R7 and R7.3 chemistries and different sequencing kits and compare the resulting, synthetic reads, to that of other long sequence simulators and experimental ONT reads. We expect NanoSim to have an enabling role in the field and benefit the development of scalable NGS technologies for the long nanopore reads, including genome assembly, mutation detection, and even metagenomic analysis software.
DOI: 10.5524/100286
title: Supporting data for "Genome sequencing of the sweetpotato whitefly <i>Bemisia tabaci</i> MED/Q"

description: Invasive whitefly, <i>Bemisia tabaci</i>, is a highly destructive agricultural and ornamental crop pest. As a group, <i>B. tabaci</i> damages host plants through phloem feeding and vectoring plant pathogens. Introductions of <i>B. tabaci</i> are difficult to quarantine and eradicate due to high reproductive rates, broad host plant range, and resistance to chemical insecticides. A 658 Mb draft genome for the Q-type <i>B. tabaci</i> (MED/Q) assembled and annotated with 20,786 protein-coding genes. Metabolic pathways show an expansion in the number of gene family members, in particular, the cytochrome P450 monooxygenases. Additionally, amino acid biosynthesis pathways are partitioning among host and endosymbiont genomes in a manner that is distinct from other hemipteran systems, wherein evidence of horizontal gene transfer to the host genome likely form the basis of obligatory relationships. Putative loss of function of the immune deficiency (IMD) signaling pathway due to gene loss is a shared ancestral trait of hemipteran insects that show competency for hosting endosymbiotic bacteria. This expansion of P450 gene family member may influence the well-noted capacity of MED/Q to adapt to repeated exposures to chemical insecticides, and furthermore, be related to invasiveness in monoculture cropping systems where such applications are prevalent.<br>This sequencing project was a collaborative effort between BGI-shenzhen and a consortium of international whitefly researchers. Various members have corresponded extensively through e-mails and phone calls. Many aspects of the genome sequencing project were discussed including the choice of <i>B. tabaci</i> cryptic species to propose. The researchers collectively decided that given the many resources already developed, the global invasion status and the large number of scientists studying them, the Q-type <i>B. tabaci</i> (MED/Q) would be the best choice. We expect that fairly extensive studies can be undertaken on other cryptic species of <i>B. tabaci</i> through the use of heterologous sequences once the <i>B. tabaci</i> Q genome sequence is available.