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Li Charlie Xia, Dongmei Ai, Hojoon Lee, Noemi Andor, Chao Li, Nancy R Zhang, Hanlee P Ji
Background: Simulating genome sequence data with variant features facilitates the development and benchmarking of structural variant analysis programs. However, there are only a few data simulators that provide structural variants in silico and even fewer that provide variants with different allelic fraction and haplotypes. Findings: We developed SVEngine, an open source tool to address this need. SVEngine simulates next generation sequencing data with embedded structural variations...
July 5, 2018: GigaScience
Julia M Huntenburg, Christopher J Steele, Pierre-Louis Bazin
With recent improvements in human magnetic resonance imaging (MRI) at ultra-high fields, the amount of data collected per subject in a given MRI experiment has increased considerably. Standard image processing packages are often challenged by the size of these data and dedicated methods are needed to leverage their extraordinary spatial resolution. Here we introduce a flexible Python toolbox which implements a set of advanced techniques for high-resolution neuroimaging. With these tools, segmentation and laminar analysis of cortical MRI data can be performed at resolutions up to 500 μm in reasonable times...
July 4, 2018: GigaScience
Breon M Schmidt, Nadia M Davidson, Anthony D K Hawkins, Ray Bartolo, Ian J Majewski, Paul G Ekert, Alicia Oshlack
Background: Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes. While there are many methods for identifying fusion genes from RNA-seq data, visualising these transcripts and their supporting reads remains challenging. Findings: Clinker is a bioinformatics tool written in Python, R and Bpipe, that leverages the superTranscript method to visualise fusion genes. We demonstrate the use of Clinker to obtain interpretable visualisations of the RNA-seq data that lead to fusion calls...
July 4, 2018: GigaScience
Angela Ballantyne
Being asked to write about the ethics of big data is a bit like being asked to write about the ethics of life. Big data is now integral to so many aspects of our daily lives-communication, social interaction, medicine, access to government services, shopping and navigation. Given this diversity, there is no one-size-fits-all framework for how to ethically manage your data. Wih that in mind, here I attempt to present seven ethical values for responsible data use.
June 28, 2018: GigaScience
Marcela M Fernandez-Gutierrez, David B H van Zessen, Peter van Baarlen, Michiel Kleerebezem, Andrew P Stubbs
Background: In vitro scratch assays have been widely used to study the influence of bioactive substances on the processes of cell migration and proliferation that are involved in re-epithelialization. The development of high-throughput microscopy and image analysis has enabled scratch assays to become compatible with high-throughput research. However, effective processing and in-depth analysis of such high-throughput image-datasets is far from trivial and requires integration of multiple image processing and data extraction software tools...
June 28, 2018: GigaScience
Yang-Min Kim, Jean-Baptiste Poline, Guillaume Dumas
Reproducibility has been shown to be limited in many scientific fields. This question is a fundamental tenet of scientific activity, but the related issues of reusability of scientific data are poorly documented. Here, we present a case study of our difficulties to reproduce a published bioinformatics method even though code and data were available. First, we tried to re-run the analysis with the code and data provided by the authors. Second, we reimplemented the whole method in a Python package to avoid dependency on a MATLAB license and ease the execution of the code on a HPCC (High-Performance Computing Cluster)...
June 28, 2018: GigaScience
Ram Krishna Shrestha, Pingtao Ding, Jonathan Dg Jones, Dan MacLean
Background: ATAC-cap-seq is a high-throughput sequencing method that combines ATAC-seq with targeted nucleic acid enrichment of precipitated DNA fragment. There are increased analytical difficulties arising from working with a set of regions of interest that may be small in number and biologically dependent. Common statistical pipelines for RNAseq might be assumed to apply but can give misleading results on ATAC-cap-seq data. A tool is needed to allow a non-specialist user to quickly and easily summarise data and apply sensible and effective normalisation and analysis...
June 28, 2018: GigaScience
Ai-Xiang Dong, Hai-Bo Xin, Zi-Jing Li, Hui Liu, Yan-Qiang Sun, Shuai Nie, Zheng-Nan Zhao, Rong-Feng Cui, Ren-Gang Zhang, Quan-Zheng Yun, Xin-Ning Wang, Fatemeh Maghuly, Ilga Porth, Ri-Chen Cong, Jian-Feng Mao
Background: Salvia splendens Ker-Gawler, scarlet or tropical sage, is a tender herbaceous perennial widely introduced and seen in public gardens all over the world. With few molecular resources, breeding is still restricted to traditional phenotypic selection, and the genetic mechanisms underlying phenotypic variation still remain unknown. Hence, a high quality reference genome will be very valuable for marker assisted breeding, genome editing or molecular genetics. Findings: We generated 66 gigabases (Gb) and 37 Gb of raw DNA sequences, respectively, from whole-genome sequencing of a largely homozygous scarlet sage inbred line using PacBio Single-Molecule Real-Time (SMRT) and Illumina HiSeq sequencing platforms...
June 19, 2018: GigaScience
Juan Sebastián Celis, Daniel Wibberg, Catalina Ramírez-Portilla, Oliver Rupp, Alexander Sczyrba, Anika Winkler, Jörn Kalinowski, Thomas Wilke
Background: Many cnidarians, including stony corals, engage in complex symbiotic associations, comprising the eukaryotic host, photosynthetic algae, and highly diverse microbial communities-together referred to as holobiont. This taxonomic complexity makes sequencing and assembling coral host genomes extremely challenging. Therefore, previous cnidarian genomic projects were based on symbiont-free tissue samples. However, this approach may not be applicable to the majority of cnidarian species for ecological reasons...
June 18, 2018: GigaScience
Carlos A Manacorda, Sebastian Asurmendi
Background: Recently, much technical progress was achieved in the field of plant phenotyping. High-throughput platforms and the development of improved algorithms for rosette image segmentation make it now possible to extract shape and size parameters for genetic, physiological and environmental studies on a large scale. The development of low-cost phenotyping platforms and freeware resources make it possible to widely expand phenotypic analysis tools for Arabidopsis. However, objective descriptors of shape parameters that could be used independently of platform and segmentation software used are still lacking and shape descriptions still rely on ad hoc or even sometimes contradictory descriptors, which could make comparisons difficult and perhaps inaccurate...
June 18, 2018: GigaScience
Fei Gao, Xue Wang, Xuming Li, Mingyue Xu, Huayun Li, Merhaba Abla, Huigai Sun, Shanjun Wei, Jinchao Feng, Yijun Zhou
Background: Ammopiptanthus nanus is a rare broad-leaved shrub in the desert and arid regions of Central Asia. This plant species exhibits extremely high tolerance to drought and freezing and has been used in abiotic tolerance research in plants. As a relic of the Tertiary period, A. nanus is of great significance to plant biogeographic research in the ancient Mediterranean region. Here we report a draft genome assembly using the PacBio platform and gene annotation for A. nanus. Findings: A total of 64...
June 18, 2018: GigaScience
Alessia Visconti, Tiphaine C Martin, Mario Falchi
YAMP is a user-friendly workflow that enables the analysis of whole shotgun metagenomic data while using containerisation to ensure computational reproducibility and facilitate collaborative research. YAMP can be executed on any UNIX-like system, and offers seamless support for multiple job schedulers as well as for Amazon AWS cloud. Although YAMP has been developed to be ready-to-use by non-experts, bioinformaticians will appreciate its flexibility, modularisation, and simple customisation. The YAMP script, parameters, and documentation are available at https://github...
June 18, 2018: GigaScience
Jue Wang, Jia-Rong Zhang, Yu-Feng Zang, Tao Wu
Background: Resting-state functional magnetic resonance imaging (RS-fMRI) has frequently been used to investigate local spontaneous brain activity in Parkinson's disease (PD) in a whole-brain, voxel-wise manner. To quantitatively integrate these studies, we conducted a coordinate-based meta-analysis (CB meta-analysis), using the seed-based d mapping (SDM) method, on 15 studies that used amplitude of low frequency fluctuation (ALFF) and 11 studies that used regional homogeneity (ReHo)...
June 18, 2018: GigaScience
L M Simon, S Karg, A J Westermann, M Engel, A H A Elbehery, B Hense, M Heinig, L Deng, F J Theis
Background: With the advent of the age of big data in bioinformatics, large volumes of data and high performance computing power enable researchers to perform re-analyses of publicly available datasets at an unprecedented scale. Ever more studies imply the microbiome in both normal human physiology and a wide range of diseases. RNA sequencing technology (RNA-seq) is commonly used to infer global eukaryotic gene expression patterns under defined conditions, including human disease-related contexts, but its generic nature also enables the detection of microbial and viral transcripts...
June 12, 2018: GigaScience
Fernando Meyer, Peter Hofmann, Peter Belmann, Ruben Garrido-Oter, Adrian Fritz, Alexander Sczyrba, Alice C McHardy
Reconstructing the genomes of microbial community members is key to the interpretation of shotgun metagenome samples. Genome binning programs deconvolute reads or assembled contigs of such samples into individual bins, but assessing their quality is difficult due to the lack of evaluation software and standardized metrics. We present AMBER, an evaluation package for the comparative assessment of genome reconstructions from metagenome benchmark data sets. It calculates the performance metrics and comparative visualizations used in the first benchmarking challenge of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI)...
June 8, 2018: GigaScience
Mian Xia, Xue Han, Hang He, Renbo Yu, Gang Zhen, Xiping Jia, Beijiu Cheng, Xing Wang Deng
Background: Luo-han-guo (Siraitia grosvenorii), also called monk fruit, is a member of the Cucurbitaceae family. Monk fruit has become an important area for research because of the pharmacological and economic potential of its non-caloric, extremely sweet components (mogrosides). It is also commonly used in traditional Chinese medicine for the treatment of lung congestion, sore throat and constipation. Recently, a single reference genome became available for monk fruit, assembled from 36...
June 8, 2018: GigaScience
Silvia Gioiosa, Marco Bolis, Tiziano Flati, Annalisa Massini, Enrico Garattini, Giovanni Chillemi, Maddalena Fratelli, Tiziana Castrignanò
Background: Gene fusions derive from chromosomal rearrangements and the resulting chimeric transcripts are often endowed with oncogenic potential. Furthermore, they serve as diagnostic tools for the clinical classification of cancer subgroups with different prognosis and, in some cases, they can provide specific drug targets. So far, many efforts have been carried out to study gene fusion events occurring in tumor samples. In recent years, the availability of a comprehensive Next Generation Sequencing dataset for all the existing human tumor cell lines has provided the opportunity to further investigate these data in order to identify novel and still uncharacterized gene fusion events...
June 1, 2018: GigaScience
Bagdevi Mishra, Deepak K Gupta, Markus Pfenninger, Thomas Hickler, Ewald Langer, Bora Nam, Juraj Paule, Rahul Sharma, Bartosz Ulaszewski, Joanna Warmbier, Jaroslaw Burczyk, Marco Thines
Background: The European Beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany. Findings: Using a hybrid assembly approach with Illumina reads with short- and long-insert libraries, coupled with long PacBio reads, we obtained an assembled genome size of 542 Mb, in line with flow cytometric genome size estimation...
May 28, 2018: GigaScience
Thomas Nind, James Galloway, Gordon McAllister, Donald Scobbie, Wilfred Bonney, Christopher Hall, Leandro Tramma, Parminder Reel, Martin Groves, Philip Appleby, Alex Doney, Bruce Guthrie, Emily Jefferson
Background: The Health Informatics Centre (HIC) at the University of Dundee provides a service to securely host clinical datasets and extract relevant data for anonymised cohorts to researchers to enable them to answer key research questions. As is common in research using routine healthcare data, the service was historically delivered using ad-hoc processes resulting in the slow provision of data whose provenance was often hidden to the researchers using it. This paper describes the development and evaluation of the Research Data Management Platform (RDMP): an open source tool to load, manage, clean, and curate longitudinal healthcare data for research and provide reproducible and updateable datasets for defined cohorts to researchers...
May 22, 2018: GigaScience
Jonathan R Belyeu, Thomas J Nicholas, Brent S Pedersen, Thomas A Sasani, James M Havrilla, Stephanie N Kravitz, Megan E Conway, Brian K Lohman, Aaron R Quinlan, Ryan M Layer
SV-plaudit is a framework for rapidly curating structural variant (SV) predictions. For each SV, we generate an image that visualizes the coverage and alignment signals from a set of samples. Images are uploaded to our cloud framework where users assess the quality of each image using a client-side web application. Reports can then be generated as a tab-delimited file or annotated Variant Call Format (VCF) file. As a proof of principle, nine researchers collaborated for 1 hour to evaluate 1,350 SVs each. We anticipate that SV-plaudit will become a standard step in variant calling pipelines and the crowd-sourced curation of other biological results...
July 1, 2018: GigaScience
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