scholarly journals IonCRAM: a reference-based compression tool for ion torrent sequence files

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Moustafa Shokrof ◽  
Mohamed Abouelhoda
Keyword(s):  
Data Transfer ◽  
Clinical Test ◽  
Ion Torrent ◽  
Space Saving ◽  
Ion Torrent Sequencing ◽  
The Cost ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Missing Feature

Abstract Background Ion Torrent is one of the major next generation sequencing (NGS) technologies and it is frequently used in medical research and diagnosis. The built-in software for the Ion Torrent sequencing machines delivers the sequencing results in the BAM format. In addition to the usual SAM/BAM fields, the Ion Torrent BAM file includes technology-specific flow signal data. The flow signals occupy a big portion of the BAM file (about 75% for the human genome). Compressing SAM/BAM into CRAM format significantly reduces the space needed to store the NGS results. However, the tools for generating the CRAM formats are not designed to handle the flow signals. This missing feature has motivated us to develop a new program to improve the compression of the Ion Torrent files for long term archiving. Results In this paper, we present IonCRAM, the first reference-based compression tool to compress Ion Torrent BAM files for long term archiving. For the BAM files, IonCRAM could achieve a space saving of about 43%. This space saving is superior to what achieved with the CRAM format by about 8–9%. Conclusions Reducing the space consumption of NGS data reduces the cost of storage and data transfer. Therefore, developing efficient compression software for clinical NGS data goes beyond the computational interest; as it ultimately contributes to the overall cost reduction of the clinical test. The space saving achieved by our tool is a practical step in this direction. The tool is open source and available at Code Ocean, github, and http://ioncram.saudigenomeproject.com.

scholarly journals RETRACTED: LFQC: a lossless compression algorithm for FASTQ files

2014 ◽  
Vol 35 (9) ◽  
pp. e1-e7
Author(s):  
Sudipta Pathak ◽  
Sanguthevar Rajasekaran
Keyword(s):  
State Of The Art ◽  
Compression Algorithm ◽  
Genomic Research ◽  
Sequencing Technology ◽  
Compression Algorithms ◽  
Average Improvement ◽  
The Cost ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

Abstract Motivation Next-generation sequencing (NGS) technologies have revolutionized genomic research by reducing the cost of whole-genome sequencing. One of the biggest challenges posed by modern sequencing technology is economic storage of NGS data. Storing raw data is infeasible because of its enormous size and high redundancy. In this article, we address the problem of storage and transmission of large Fastq files using innovative compression techniques. Results We introduce a new lossless non-reference-based fastq compression algorithm named lossless FastQ compressor. We have compared our algorithm with other state of the art big data compression algorithms namely gzip, bzip2, fastqz, fqzcomp, G-SQZ, SCALCE, Quip, DSRC, DSRC-LZ etc. This comparison reveals that our algorithm achieves better compression ratios. The improvement obtained is up to 225%. For example, on one of the datasets (SRR065390_1), the average improvement (over all the algorithms compared) is 74.62%. Availability and implementation The implementations are freely available for non-commercial purposes. They can be downloaded from http://engr.uconn.edu/∼rajasek/FastqPrograms.zip.

scholarly journals Streaming Support for Data Intensive Cloud-Based Sequence Analysis

2013 ◽  
Vol 2013 ◽  
pp. 1-16 ◽  
Author(s):  
Shadi A. Issa ◽  
Romeo Kienzler ◽  
Mohamed El-Kalioby ◽  
Peter J. Tonellato ◽  
Dennis Wall ◽  
...  
Keyword(s):  
Cloud Computing ◽  
Data Transfer ◽  
Cost Effective ◽  
Workflow Systems ◽  
Data Intensive ◽  
Computing Services ◽  
Cloud Computing Services ◽  
Computational Resources ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data

Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client’s site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide theelastreampackage that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation.

Primary varicose veins

Phlebologie ◽  
2010 ◽  
Vol 39 (03) ◽  
pp. 133-137
Author(s):  
H. Partsch
Keyword(s):  
Varicose Veins ◽  
Compression Therapy ◽  
Daily Practice ◽  
Clinical Severity ◽  
Compression Stockings ◽  
Primary Varicose Veins ◽  
The Cost ◽  
Convincing Data ◽  
Long Term Studies

SummaryBackground: Compression stockings are widely used in patients with varicose veins. Methods: Based on published literature three main points are discussed: 1. the rationale of compression therapy in primary varicose veins, 2. the prescription of compression stockings in daily practice, 3. studies required in the future. Results: The main objective of prescribing compression stockings for patients with varicose veins is to improve subjective leg complaints and to prevent swelling after sitting and standing. No convincing data are available concerning prevention of progression or of complications. In daily practice varicose veins are the most common indication to prescribe compression stockings. The compliance depends on the severity of the disorder and is rather poor in less severe stages. Long-term studies are needed to proof the cost-effectiveness of compression stockings concerning subjective symptoms and objective signs of varicose veins adjusted to their clinical severity. Conclusion: Compression stockings in primary varicose veins are able to improve leg complaints and to prevent swelling.

An Evaluation of Provincial Macroeconomic Performance in Vietnam

2017 ◽  
pp. 34-47
Author(s):  
Hoi Le Quoc ◽  
Nam Pham Xuan ◽  
Tuan Nguyen Anh
Keyword(s):  
Development Strategy ◽  
Institutional Transformation ◽  
Economic Indicators ◽  
Macroeconomic Performance ◽  
Economic Development Strategy ◽  
Socio Economic Development ◽  
The Cost ◽  
Development Objectives ◽  
First Time

The study was targeted at developing a methodology for constructing a macroeconomic performance index at a provincial level for the first time in Vietnam based on 4 groups of measurements: (i) Economic indicators; (ii) oriented economic indicators; (iii) socio-economic indicators; and (iv) economic - social – institutional indicators. Applying the methodology to the 2011 - 2015 empirical data of all provinces in Vietnam, the research shows that the socio-economic development strategy implemented by those provinces did not provide balanced outcomes between growth and social objectives, sustainability and inclusiveness. Many provinces focused on economic growth at the cost of structural change, equality and institutional transformation. In contrast, many provinces were successful in improving equality but not growth. Those facts threaten the long-term development objectives of the provinces.

scholarly journals Patient Derived Xenografts for Genome-Driven Therapy of Osteosarcoma

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 416
Author(s):  
Lorena Landuzzi ◽  
Maria Cristina Manara ◽  
Pier-Luigi Lollini ◽  
Katia Scotlandi
Keyword(s):  
Clinical Trials ◽  
Tumor Heterogeneity ◽  
Functional Studies ◽  
Ngs Data Analysis ◽  
The Many ◽  
Orthotopic Xenografts ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing ◽  
Somatic Copy Number Alterations

Osteosarcoma (OS) is a rare malignant primary tumor of mesenchymal origin affecting bone. It is characterized by a complex genotype, mainly due to the high frequency of chromothripsis, which leads to multiple somatic copy number alterations and structural rearrangements. Any effort to design genome-driven therapies must therefore consider such high inter- and intra-tumor heterogeneity. Therefore, many laboratories and international networks are developing and sharing OS patient-derived xenografts (OS PDX) to broaden the availability of models that reproduce OS complex clinical heterogeneity. OS PDXs, and new cell lines derived from PDXs, faithfully preserve tumor heterogeneity, genetic, and epigenetic features and are thus valuable tools for predicting drug responses. Here, we review recent achievements concerning OS PDXs, summarizing the methods used to obtain ectopic and orthotopic xenografts and to fully characterize these models. The availability of OS PDXs across the many international PDX platforms and their possible use in PDX clinical trials are also described. We recommend the coupling of next-generation sequencing (NGS) data analysis with functional studies in OS PDXs, as well as the setup of OS PDX clinical trials and co-clinical trials, to enhance the predictive power of experimental evidence and to accelerate the clinical translation of effective genome-guided therapies for this aggressive disease.

Evaluation attempt of own body sensing amongst persons with and without scoliosis

2021 ◽  
pp. 1-6
Author(s):  
Elżbieta Szczygieł ◽  
Agata Gigoń ◽  
Izabela Cebula Chudyba ◽  
Golec Joanna ◽  
Golec Edward
Keyword(s):  
Idiopathic Scoliosis ◽  
Sensory Integration ◽  
Head Position ◽  
Clinical Test ◽  
Spine Deformity ◽  
Functional Tests ◽  
Body Proportion ◽  
Average Value ◽  
Age Range

BACKGROUND: Adolescent idiopathic scoliosis (AIS) is a common structural spine deformity affecting 2%–4% of adolescents. Due to the unknown cause of idiopathic scoliosis, its therapy is a long-term and often unsatisfactory process. In the literature, it is often suggested that problems related to the feeling of one’s own body are caused by AIS. OBJECTIVE: The aim of this study was to assess the feeling of one’s own body among children with and without scoliosis on the example of feeling the head position, pelvis shape and balance. METHOD: The research included 62 children: 30 with scoliosis and 25 without diagnosed scoliosis with an age range between 11 to 19 years. The minimum scoliosis value was 7∘ and the maximum was 53∘. The average value was 25∘. During the study, three functional tests were used: Cervical Joint Position Error Test (CJPET), Clinical Test of Sensory Integration on Balance (CTSIB) and Body proportion demonstration test (BPDT). RESULTS: The results of the tests showed statistically significant differences (CJPET p= 3.54* 10-14, CTSIB p= 0.0376, BPDT p= 0.0127). However, none of the studies showed a correlation between the results of people with scoliosis and the value of their Cobb angles.

Empowering and Directive Leadership: The Cost of Changing Styles

2021 ◽  
pp. 227853372110083
Author(s):  
Smita Mukherjee ◽  
Zubin R. Mulla
Keyword(s):  
Laboratory Experiment ◽  
Leadership Styles ◽  
Leadership Style ◽  
Affective Commitment ◽  
Team Outcomes ◽  
History Of ◽  
Satisfaction With The Leader ◽  
The Cost ◽  
First Time

We examine the cost of leaders changing between empowering and directive leadership styles on team outcomes. In a laboratory experiment, we collected data from 240 participants in 80 teams. Confederates enacted different leadership styles and led teams of participants in performing a series of tasks. When leaders changed their style from directive to empowering, teams took time to respond in terms of higher satisfaction with leader and affective commitment. However, when leaders changed their style from empowering to directive, the deterioration of satisfaction with leader and reduction in affective commitment were immediate. Moreover, teams of leaders who had been consistently directive showed higher affective commitment as compared to teams of leaders who had a history of being empowering but later shifted to being directive. First time managers can get inputs on how they should enact their leadership style and be aware that switching between styles may impose long-term costs on the team’s affective commitment and satisfaction with the leader.

scholarly journals Domain Adaptation for Semantic Segmentation of Historical Panchromatic Orthomosaics in Central Africa

2021 ◽  
Vol 10 (8) ◽  
pp. 523
Author(s):  
Nicholus Mboga ◽  
Stefano D’Aronco ◽  
Tais Grippa ◽  
Charlotte Pelletier ◽  
Stefanos Georganos ◽  
...  
Keyword(s):  
Land Cover ◽  
Domain Adaptation ◽  
Central Africa ◽  
Semantic Segmentation ◽  
Target Domain ◽  
Convolutional Networks ◽  
Fully Convolutional Networks ◽  
The Cost ◽  
Performance Gains

Multitemporal environmental and urban studies are essential to guide policy making to ultimately improve human wellbeing in the Global South. Land-cover products derived from historical aerial orthomosaics acquired decades ago can provide important evidence to inform long-term studies. To reduce the manual labelling effort by human experts and to scale to large, meaningful regions, we investigate in this study how domain adaptation techniques and deep learning can help to efficiently map land cover in Central Africa. We propose and evaluate a methodology that is based on unsupervised adaptation to reduce the cost of generating reference data for several cities and across different dates. We present the first application of domain adaptation based on fully convolutional networks for semantic segmentation of a dataset of historical panchromatic orthomosaics for land-cover generation for two focus cities Goma-Gisenyi and Bukavu. Our experimental evaluation shows that the domain adaptation methods can reach an overall accuracy between 60% and 70% for different regions. If we add a small amount of labelled data from the target domain, too, further performance gains can be achieved.

scholarly journals Evaluation of Ion Torrent next-generation sequencing for thalassemia diagnosis

2020 ◽  
Vol 48 (12) ◽  
pp. 030006052096777
Author(s):  
Peisong Chen ◽  
Xuegao Yu ◽  
Hao Huang ◽  
Wentao Zeng ◽  
Xiaohong He ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ion Torrent ◽  
Next Generation ◽  
Large Deletions ◽  
Different Types ◽  
Variant Detection ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs ◽  
Accuracy And Repeatability ◽  
Generation Sequencing

Introduction To evaluate a next-generation sequencing (NGS) workflow in the screening and diagnosis of thalassemia. Methods In this prospective study, blood samples were obtained from people undergoing genetic screening for thalassemia at our centre in Guangzhou, China. Genomic DNA was polymerase chain reaction (PCR)-amplified and sequenced using the Ion Torrent system and results compared with traditional genetic analyses. Results Of the 359 subjects, 148 (41%) were confirmed to have thalassemia. Variant detection identified 35 different types including the most common. Identification of the mutational sites by NGS were consistent with those identified by Sanger sequencing and Gap-PCR. The sensitivity and specificities of the Ion Torrent NGS were 100%. In a separate test of 16 samples, results were consistent when repeated ten times. Conclusion Our NGS workflow based on the Ion Torrent sequencer was successful in the detection of large deletions and non-deletional defects in thalassemia with high accuracy and repeatability.

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