cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100173
title: AsmVar: tools and exemplar data.

description: Comprehensive characterization of genomic variation in a human individual is important for understanding disease and for development of personalized approaches to treatment. Many tools exist for identification of single nucleotide polymorphism (snps), small indels and large deletions based on DNA re-sequencing strategy. However, those approaches consistently display significant bias for recovery of complex structural variants and novel sequence in the individual genomes and lack sequence interpretation such as ancestral state and mechanism. Here we present a novel approach implemented in a single software package, AsmVar, to discover, genotype and characterize different forms of structural variants and novel sequence in population-scale de novo assemblies at single nucleotide resolution. Our approach displays good scalability and makes it applicable for investigations in large population studies of species with complex genomes, such as homo sapiens. Application of AsmVar to several human de novo assemblies captures a wide spectrum of structural variants and novel sequences present in the human population with high sensitivity and specificity. Our method provides a direct solution to investigate the structural variations and novel sequences from <em>de novo</em> assemblies, which is important for construction of population-scale pan genome. Our study also suggests the advantages of the <em>de novo</em> assembly strategy for definition of genome structure. <br> This software has been released under the 
 MIT License Copyright 2014-2015.
<br>
DOI: 10.5524/100176
title: Supporting data for "Enhanced reproducibility of SADI Web service workflows with Galaxy and Docker".

description: Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services.<br>The GigaScience article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration. <br>Here we host links to the current github repository for the most upto date version, in addition we host an archival version of the gihub repository as it was at the time of publication.
DOI: 10.5524/100177
title: Supporting data for "A single chromosome assembly of <em>Bacteroides fragilis</em> strain BE1 from Illumina and MinION nanopore sequencing data."

description: Second and third generation sequencing technologies have revolutionised bacterial genomics. Short-read Illumina reads result in cheap but fragmented assemblies, whereas longer reads are more expensive but result in more complete genomes. The Oxford Nanopore MinION device is a revolutionary mobile sequencer that can produce thousands of long, single molecule reads.<br>
We sequenced <em>Bacteroides fragilis</em> strain BE1 using both the Illumina MiSeq and Oxford Nanopore MinION platforms. We were able to assemble a single chromosome of 5.18 Mb, with no gaps, using publicly available software and commodity computing hardware. We identified gene rearrangements and the state of invertible promoters in the strain. <br>
The final assembly and annotations are available from the public archives (EBI/NCBI/DDBJ) and additionally here we provide the assemblies done for comparison from each of the individual technologies and the alignments of the original raw reads to the final assembly.<br>
DOI: 10.5524/100178
title: Supporting materials and software for "GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists".

description: K-mer-based methods of genome analysis have attracted great interest because they do not require genome assembly and can be performed directly on sequencing reads. Many analysis tasks require one to compare k-mer lists from different sequences to find words that are either unique to a specific sequence or common to many sequences. However, no stand-alone k-mer analysis tool currently allows one to perform these algebraic set operations.<br>
We have developed the GenomeTester4 toolkit, which contains a novel tool (<em>GListCompare</em>) for performing union, intersection and complement (difference) set operations on k-mer lists. We provide examples of how these general operations can be combined to solve a variety of biological analysis tasks.<br>
DOI: 10.5524/100180
title: Supporting data for "Multi-platform microRNA profiling of hepatoblastoma patients using formalin fixed paraffin embedded archival samples".

description: Formalin fixed paraffin embedded (FFPE) samples are a valuable resource in cancer research and have the potential to be extensively used. However, they are often underused because of degradation and chemical modifications occurring in the RNA that can present obstacles in downstream analysis. In routine medical care, FFPE material is examined and archived, therefore clinical collections of many types of cancers exist. It is beneficial to assess and record the quality of data that can be obtained from this type of material. The current study investigated three independent platforms and their ability to profile microRNAs (miRNAs) within FFPE samples from hepatoblastoma (HB) patients.
Here we present three types of dataset consisting of miRNA profiles for 13 HB patients with different tumour types and molecular variations. The three platforms that were used to generate these data are: next-generation sequencing (Illumina MiSeq), microarray (Affymetrix® GeneChip® miRNA 3.0 array) and NanoString (nCounter, Human v2 miRNA Assay). The mature miRNAs identified are based on miRBase version 17 and 18.
These datasets provide a global landscape of miRNA expression for a rare childhood cancer that has not previously been well characterised. These data could serve as a resource for future studies aiming to make comparisons of HB miRNA profiles and to document aberrant miRNA expression in this type of cancer.
DOI: 10.5524/100181
title: Supporting data for "Genomic analyses revealFAM84B and the NOTCH pathway are associated with the progression of esophageal squamous cell carcinoma".

description: Esophageal squamous cell carcinoma (ESCC) is the sixth most lethal cancer worldwide and the fourth most lethal cancer in China. Although copy number alterations and somaticpoint mutations associated with the development of ESCC have been identified by array-based technologies and genome-wide studies respectively. The genomic characterization of ESCC from different stages of the disease has not been explored and is likely to reveal additional oncogenic mechanisms. Here we have performed either whole-genome sequencing or whole-exome sequencing on 51 stage I and 53 stage III ESCC patients to characterize the genomic alterations that occur during the various clinical stages of ESCC, and further validated these changes in 36 atypical hyperplasia samples. <br>
Due to the sensitive nature of this dataset it is being hosted in the secure restricted access database European Genome-Phenome Archive at the EBI. It has been assigned the accession number EGAD00001001487. <br>
To gain access to this dataset you will need to apply for permission from the Shanxi Medical University and BGI Data Access Committee (DAC). 
There are two forms available to download from GigaDB FTP server (below), both should be completed and emailed to Dr Yongping Cui, who is the named representative of the combined Shanxi Medical Uni and BGI DAC. <br>
After sending the forms to the DAC you will be contacted either by the DAC to decline your application or from the EGA with login details if your application is approved. This process can take several days.<br>
DOI: 10.5524/100185
title: Supporting data for "Species level resolution of 16S rRNA gene amplicons sequenced through MinION portable nanopore sequencer".

description: The miniaturized and portable DNA sequencer MinION has been released to the scientific community in the framework of an early access programme to evaluate its application for a wide variety of genetic approaches. This technology has demonstrated a great potential, especially in genome-wide analyses. In this study, we tested the ability of the MinION system to perform amplicon sequencing in order to design new approaches to study microbial diversity using nearly full-length 16S rDNA sequences.<br>
Using the R7.3 chemistry, we generated more than 3.8 million events (nt) during a single sequencing run. This data was sufficient for reconstruction of more than 90% of the 16S rRNA gene sequences for 20 different species present in a mock community used as a reference. After read mapping and 16S rRNA gene assembly, consensus sequences and 2d reads were recovered to make taxonomy assignments down to the species level. Additionally, we were able to measure the relative abundance of all the species present in a mock community and detected a biased species distribution originating from the PCR reaction using "universal" primers.<br>
Although nanopore-based sequencing produces reads with lower per-base accuracy in comparison with other platforms, the MinION DNA sequencer is valuable for both high taxonomic resolution and microbial diversity analysis. Improvements of the nanopore chemistry will further deliver more reliable information useful for the specific detection of microbial species and strains in complex ecosystems as a consequence of minimizing the basecalling errors and nucleotide bias as that reported here for 16S rRNA amplicon sequencing.
DOI: 10.5524/100186
title: Supporting data for the "Draft genome of the Chinese mitten crab, <em>Eriocheir sinensis</em>".

description: The Chinese mitten crab,<em> Eriocheir sinensis</em>, is one of the most economically important representatives of the Crustacea in China, and an invasive species in much of Europe and North America. Its transition from swimming type to crawling during its early development process, anadromous migration for growth, and catadromous migration for breeding make it an attractive model for research. However, knowledge about the underlying molecular mechanisms to regulate these processes is still very limited. A total of 258.8-Gb raw reads for crab whole-genome sequencing were generated using the Illumina HiSeq2000 platform, and available from the SRA. Here we report the final genome assembly (1.12 Gb), about 67.5% of the estimated genome size (1.66 Gb), and composed of 17,553 scaffolds (&gt;2 kb) with a N50 of 224 kb. We identified 14,436 genes using AUGUSTUS, of which 7,549 were shown to have significant supporting evidence using the Glean pipeline. This gene number is much higher than that of the Horseshoe crab (see GigaDB dataset 100091) and the annotation completeness evaluated by CEGMA is 66.9%.
DOI: 10.5524/100188
title: Supporting materials for "Whole genome sequence analysis of BT-474 using Complete Genomics’ standard and Long Fragment Read technologies".

description: The cell line BT-474 is a popular cell line for studying the biology of cancer and developing novel drugs. However, there is no published complete genome sequence for this highly utilized scientific resource. In this study we sought to provide a comprehensive and useful data set for the scientific community by generating a whole genome sequence for BT-474.
Genomic DNA was isolated from an early passage of the BT-474 cell line and 5 ug was used to generate a 114X coverage whole genome sequence using Complete Genomics standard sequencing process. In order to provide additional variant phasing and structural variation data we also processed and analyzed two separate libraries of 5 and 6 individual cells to depths of 99X and 87X, respectively using Complete Genomics Long Fragment Read technology (LFR). 
BT-474 is a highly aneuploid cell line with an extremely complex genome sequence. By generating ~300X total coverage we have generated a much more complete understanding, at the genomic level, of this highly utilized cell line.
DOI: 10.5524/100189
title: Supporting information for "Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)".

description: Domesticated apple (Malus domestica Borkh) is a popular temperate fruit with high levels of nutrients and a diversity of flavors. In 2012, global apple production accounted for at least one tenth of all harvested fruits. A high-quality apple genome assembly is crucial for the selection and breeding of new cultivars. Currently, there is only a single genome reference available for apple, assembled from 16.9 genome coverage short reads via Sanger and 454 sequencing technologies. Although this is a useful resource, this assembly covers only ~89% of the non-repetitive portion of the genome, and has a relatively short (16.7 kb) contig N50 length. These downsides make it difficult to apply this reference in transcriptive or whole-genome re-sequencing
analyses.<br>
Here we present an improved hybrid de novo genomic assembly of apple (Golden Delicious), which was obtained from 76 Gb (~ 102 genome coverage) Illumina HiSeq data and 21.7 Gb (~ 29 genome coverage) PacBio data. The final draft genome is approximately 632.4 Mb, representing ~ 90 % of the estimated genome. The contig N50 size is 111,619 bp, representing a 7 fold improvement. Further annotation analyses predicted 53,922 protein-coding genes and 2,765 non-coding RNA genes. <br>
The new apple genome assembly will serve as a valuable resource for investigating complex apple traits at the genomic level. It is not only suitable for
genome editing and gene cloning, but also for RNA-seq and whole-genome resequencing studies.
DOI: 10.5524/100190
title: Micro-computed tomography scans and virtual histological slides of a recently described land planarian species of Obama otavioi (Platyhelminthes).

description: We investigated whether images obtained through X-ray micro-computed tomography (CT), can be used in conjunction with traditional methods for morphological studies of soft-bodied land planarians. Among its virtues, CT is non-invasive and provides true to scale three-dimensional imagery at high resolution. We compared these CT-based images with those obtained from light microphotography of histological sections, most of which were also digitizseddigitized at high magnification.
The specimens studied were collected in 2012. Subsequent CT-based images of the stained body of a paratype show nearly all morphological features provided by traditional histology, with the exception of structures particularly minute, 5 m, such as the sensory pits and single muscle fibers, which are best visible on traditional histological sections. Since the technique is non-destructive, the scanned specimen is preserved without damage. The raw and derivative µCT data and virtual histological sections can be found here.
DOI: 10.5524/100191
title: Imagery data of paired shrub-open microsites within the Carrizo Plain National Monument

description: Carrizo Plain National Monument is one of the largest remaining patches of San Joaquin Desert left within the Central Valley of California. It is home to many threatened and endangered species including the San Joaquin kit fox, blunt-nosed leopard lizard, and giant kangaroo rat. The dominant plant lifeform is shrubs. The species Ephedra californica comprises a major proportion of the community within this region and likely also provides key ecosystem services. We used motion sensor trail cameras to examine interactions between animals and these shrubs. This technology is a less invasive alternative to other animal surveying methods such as line transects, radio tracking, and spotlight surveys. Cameras were placed within the shrub understory and in the open (i.e. non-canopied) microhabitats at ground level to estimate animal activity.
<br>
Trail cameras were successful in detecting the presence of animal species at shruband open microhabitats. A total of 20 cameras were deployed from April 1st, 2015 to July 5th, 2015 at paired shrub/open microsites at three locations along Elkhorn Road in Carrizo Plain National Monument (35.1914 N, 119.7929 W). Each independent site was approximately 1 square kilometer. Over 420,000 pictures (both of animals and triggers from vegetation moving in the wind) were taken during this time. The trigger rate was very high on the medium sensitivity camera setting in this desert ecosystem, and the rates did not differ between shrub and open microsites.<br> We reviewed 100,000 of the images for content before uploading them to GigaDB to ensure image quality, presence of animals, date and temperature stamp, and data integrity.
It was found that some of the cameras had not had the date set correctly, users are advised to only use the dates as listed in the sampling metadata table as provided in GigaDB.<br>
There are 467 individual compressed directories of camera trap images, each directory is named according to the date it was set (YYMMDD) followed by its microsite type (shrub or open), then the site ID, shrub ID and camera ID, suffixed with .tar.gz <br>
e.g. YYMMDD_[shrub/open]_[site-ID]_[shrub-ID]_[camera-ID].tar.gz
DOI: 10.5524/100192
title: Genomic data of Pearl Millet (<em>Pennisetum glaucum</em>).

description: Pearl millet is a highly cross-pollinated diploid (2n=2x=14) C4 grass. It has high photosynthetic efficiency and biomass production potential. It is an important cereal cultivated as a staple food grain and source of straw for fodder and fuel in arid and semi-arid regions of sub-Saharan Africa and South Asia. It is necessary to explore the pearl millets genome data to reveal its genetic features and improve the production.
<br>In our project, a pearl millet genotype Tift 23D2B1-P1-P5 was chosen for sequencing on Illumina HiSeq 2000 platform. Using SOAP denovo we assembled ~1.79 Gb of pearl millet genome with N50 884.95 kb (for scaffolds greater than 1kb). A total of 38,579 genes models, as well as genome repeats and non-coding RNA elements were estimated based on the genome sequences. The genomic data of pearl millet will provide more resources and empower pearl millet crop breeding.
DOI: 10.5524/100194
title: Supporting data for "Low coverage sequencing of three echinoderm genomes: the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis".

description: There are five major extant groups of Echinodermata: Crinoidea (feather stars and sea lillies), Ophiuroidea (brittle stars and basket stars), Asteroidea (sea stars), Echinoidea (sea urchins, sea biscuits, and sand dollars), and Holothuroidea (sea cucumbers). These animals are known for their pentaradial symmetry as adults, unique water vascular system, mutable collagenous tissues, and endoskeletons of high magnesium calcite. To our knowledge, the only echinoderm species with a genome sequence available to date is <em>Strongylocentrotus pupuratus</em> (Echinoidea). The availability of additional echinoderm genome sequences is crucial for understanding the biology of these animals.
<br>
Here we present assembled draft genomes of the brittle star <em>Ophionereis fasciata</em>, the sea star <em>Patiriella regularis</em>, and the sea cucumber <em>Australostichopus mollis</em> from Illumina sequence data with coverages of 12.5x, 22.5x, and 21.4x, respectively.
<br>
These data provide a resource for mining gene superfamilies, identifying non-coding RNAs, confirming gene losses, and designing experimental constructs. They will be important comparative resources for future genomic studies in echinoderms.
DOI: 10.5524/100195
title: Examplar data demonstrating the improvement of genome assembly and annotation by using AGOUTI.

description: Genomes sequenced using short-read, next-generation sequencing technologies are error-filled and fragmented into thousands of small contigs. These incomplete and fragmented assemblies lead to errors in gene identification, such that single genes spread across multiple contigs are annotated as separate gene models. Such biases can confound inferences about the number of genes within species, as well as gene gain and loss between species.
We present AGOUTI (Annotated Genome Optimization Using Transcriptome Information), a tool that uses RNA-seq data to simultaneously combine contigs into scaffolds and fragmented gene models into single models. We show that AGOUTI improves both the contiguity of genome assemblies and the accuracy of gene annotation, providing updated versions of each as output. Running AGOUTI on a simulated dataset, we show that it is highly accurate and that it achieves higher accuracy and contiguity compared to other existing methods.
Here we provide the software, available free of charge under the MIT license, as well as the synthetic dataset for reuse and reproducibility. For the most recent updates to the software please refer to the GitHub page .
DOI: 10.5524/100199
title: Supporting information for "Gigwa - Genotype Investigator for Genome Wide Analyses".

description: Exploring the structure of genomes and analysing their evolution is essential to understand the ecological adaptation of organisms. However, with the large amounts of data being produced by Next Generation Sequencing (NGS), computational challenges arise in terms of storage, search, sharing, analysis, and visualisation. This is particularly true regarding genomic variation studies that are currently lacking scalable and user-friendly data exploration solutions. 
Here we present Gigwa, a web-based tool which provides an easy and intuitive way to explore large amounts of genotyping data by filtering the latter based not only on variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability perspectives. Gigwa can handle multiple databases and may be deployed in either single or multi-user mode. Finally, it provides a wide range of popular export formats.
The Gigwa application is suitable to manage large amounts of genomic variations through a user-friendly web interface making such a processing widely accessible. It may either be simply deployed on a workstation or used to provide a data portal to a given community of researchers.<br>
Resources available here consist of the binary files for Gigwa V1.0beta (sole web-application, Windows bundle, OSX bundle), and the material used for benchmarking (data as VCF and CSV+SQL, VCFtools scripts, MySQL stored procedures).<br>
<br>
Please visit Gigwa website for most recent updates to this software.<br>