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Parallel computing for genome sequence processing

You Zou, Yuejie Zhu, Yaohang Li, Fang-Xiang Wu, Jianxin Wang
2021 Briefings in Bioinformatics  
The rapid increase of genome data brought by gene sequencing technologies poses a massive challenge to data processing.  ...  The purpose of this review is to investigate popular parallel programming technologies for genome sequence processing.  ...  Funding This work is supported in part by the National Natural Science Foundation of China under grants (Nos U1909208, 61732009, 61772557), Hunan Provincial Science and Technology Program (No. 2018WK4001  ... 
doi:10.1093/bib/bbab070 pmid:33822883 fatcat:a4hj2fhybrc6zlsq6xyiu6snmy

Bio-sequence analysis with cradle's 3SoC#8482; software scalable system on chip

Xiandong Meng, Vipin Chaudhary
2004 Proceedings of the 2004 ACM symposium on Applied computing - SAC '04  
The Smith-Waterman algorithm, which utilizes dynamic programming, is a common method for performing exact local alignments between two protein or DNA sequences.  ...  With the dramatically increasing amounts of genomic sequence database, there is a need for faster and more sensitive searching for sequence similarity analysis.  ...  performance RISC-like and digital signal processors on a single chip with fully software programmable and dedicated input-output processors.  ... 
doi:10.1145/967900.967941 dblp:conf/sac/MengC04 fatcat:rukqry5mg5gt5jcbp2y7ugyhae

HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis

Luis Santana-Quintero, Hayley Dingerdissen, Jean Thierry-Mieg, Raja Mazumder, Vahan Simonyan, Tom Gilbert
2014 PLoS ONE  
HIVE-hexagon implements novel approaches to exploit both characteristics of sequence space and CPU, RAM and Input/Output (I/O) architecture to quickly compute accurate alignments.  ...  Inexact alignments can take up to 90% of total CPU time in bioinformatics pipelines.  ...  the nature and biology of the next-generation sequencing, in addition to provision of datasets; Carolyn A.  ... 
doi:10.1371/journal.pone.0099033 pmid:24918764 pmcid:PMC4053384 fatcat:xw3gg4d52vgfhn2u4eq5256g6y

A high performance grid-web service framework for the identification of 'conserved sequence tags'

Paolo D'Onorio De Meo, Danilo Carrabino, Nico Sanna, Tiziana Castrignano, Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Matteo Re, Flavio Mignone, Graziano Pesole
2007 Future generations computer systems  
This work shows a tool for the identification and functional annotation of 'Conserved Sequence Tags' (CSTs) through cross-species genome comparisons, deployed on a Grid System Architecture, based on Web  ...  An emerging solution is grid technology, which allows organization to make better use of existing computing resources by providing them with a single, transparent, aggregated source of computing power.  ...  Such a tool make use of local executables to perform CSTs search and is dynamically interconnected to Ensembl genomes.  ... 
doi:10.1016/j.future.2006.07.012 fatcat:lk4we4mzvnbg3hlbu77lzyoto4

CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing

Omer An, Kar-Tong Tan, Ying Li, Jia Li, Chan-Shuo Wu, Bin Zhang, Leilei Chen, Henry Yang
2020 International Journal of Molecular Sciences  
A variety of computational tools have been developed to analyse the vastly growing NGS data, which often require bioinformatics skills, tedious work and a significant amount of time.  ...  Next-generation sequencing (NGS) has been a widely-used technology in biomedical research for understanding the role of molecular genetics of cells in health and disease.  ...  Acknowledgments: We are very grateful to all the lab members of CSI Singapore NUS for their usage, feedback and support of CSI NGS Portal.  ... 
doi:10.3390/ijms21113828 pmid:32481589 pmcid:PMC7312552 fatcat:ol3ctyfx2vcntpsnyhb6lu3b5y

GenoVault: a cloud based genomics repository

Sankalp Jain, Amit Saxena, Suprit Hesarur, Kirti Bhadhadhara, Neeraj Bharti, Sunitha Manjari Kasibhatla, Uddhavesh Sonavane, Rajendra Joshi
2021 BioData Mining  
The data is uploaded by the user in individual containers that include raw read files (fastq), processed alignment files (bam, sam, bed) and the output of variation detection (vcf).  ...  GenoVault architecture allows verification of the data in terms of integrity and authentication before making it available to collaborators as per the user's permissions.  ...  The authors also acknowledge Justas Balcas for providing permission to use the Fast Data Transfer (FDT) protocol libraries.  ... 
doi:10.1186/s13040-021-00268-5 fatcat:3dxtegcrujeaxg66ovjsq7x4ge

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel (+43 others)
2020 Briefings in Bioinformatics  
To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus.  ...  However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19.  ...  The workflow itself is implemented using Snakemake [48] , which provides advanced job balancing and input/output control mechanisms, and uses conda [28] to provide well-defined and harmonized software  ... 
doi:10.1093/bib/bbaa232 pmid:33147627 fatcat:uhaen7tgtndflagcwbrvhwbcje

Cloudgene: A graphical execution platform for MapReduce programs on private and public clouds

Sebastian Schönherr, Lukas Forer, Hansi Weißensteiner, Florian Kronenberg, Günther Specht, Anita Kloss-Brandstätter
2012 BMC Bioinformatics  
The MapReduce framework enables a scalable processing and analyzing of large datasets by distributing the computational load on connected computer nodes, referred to as a cluster.  ...  In Bioinformatics, MapReduce has already been adopted to various case scenarios such as mapping next generation sequencing data to a reference genome, finding SNPs from short read data or matching strings  ...  including the complete configuration setup (input/output parameters, execution times, results) and (3) the possibility to concatenate different MapReduce jobs to pipelines.  ... 
doi:10.1186/1471-2105-13-200 pmid:22888776 pmcid:PMC3532373 fatcat:tc7jppaw3jc2jh7wwlbbxkzlzm

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis

Vahan Simonyan, Raja Mazumder
2014 Genes  
HIVE consists of a web-accessible interface for authorized users to deposit, retrieve, share, annotate, compute and visualize Next-generation Sequencing (NGS) data in a scalable and highly efficient fashion  ...  The High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-based infrastructure developed for the storage and analysis of genomic and associated biological data.  ...  Acknowledgements We would like to acknowledge the following people for providing feedback and HIVE support:  ... 
doi:10.3390/genes5040957 pmid:25271953 pmcid:PMC4276921 fatcat:fpkwi7qj6bhkxp6y3k2nxv2lre

Best Practices for Data Sharing in Phylogenetic Research

Karen Cranston, Luke J. Harmon, Maureen A. O'Leary, Curtis Lisle
2014 PLOS Currents  
We define phylogenetic data as the inputs, outputs and methodological details of a phylogenetic analysis. Current practices for publication of these data too often limit reusability.  ...  Because of these (and other) problems, phylogenetic comparative studies can be difficult or impossible to replicate or expand upon.  ...  Acknowledgements During assembly of these guidelines, we asked the community to contribute rules that would benefit their efforts in phylogenetic data publishing, reviewing or integration.  ... 
doi:10.1371/currents.tol.bf01eff4a6b60ca4825c69293dc59645 pmid:24987572 pmcid:PMC4073804 fatcat:b2k4wmv7nra7neqoee74jejrdm

A generalizable experimental framework for automated cell growth and laboratory evolution [article]

Brandon G Wong, Christopher P Mancuso, Szilvia Kiriakov, Caleb J Bashor, Ahmad S Khalil
2018 bioRxiv   pre-print
In the post-genomics era, exploration of phenotypic adaptation is limited by our ability to experimentally control selection conditions, including multi-variable and dynamic pressure regimes.  ...  Here we describe eVOLVER, a multipurpose, scalable DIY framework that can be easily configured to conduct a wide variety of growth fitness experiments at scale and cost.  ...  Wong, and members of the Khalil Lab for insightful comments on the manuscript. This work was supported by a NSF CAREER Award (MCB-1350949 to A.S.K.) and a DARPA grant (HR0011-15-C-0091 to A.S.K.).  ... 
doi:10.1101/280867 fatcat:gnjpzfbpnrdw7cuosntcsb6yqy

Improving Bio-technology Processes Using Computational Techniques [chapter]

Avinash Shankaranarayanan, Christine Amaldas
2011 Systems and Computational Biology - Bioinformatics and Computational Modeling  
Grid computing is a more complicated infrastructure that provides better efficiency than cluster computing as it tries to improve upon scalability through the dynamic addition of new nodes and efficient  ...  A two-fold speedup can be observed based on running agents in virtual machines as the input/output data access time is cut by half as resources and data were made available locally to the agents using  ...  The two volumes of this book present a series of high-quality research or review articles in a timely fashion to this emerging research field of our scientific community.  ... 
doi:10.5772/19285 fatcat:fycsazpaifhylo3aucqa7i3lgm

Big Data: Astronomical or Genomical?

Zachary D. Stephens, Skylar Y. Lee, Faraz Faghri, Roy H. Campbell, Chengxiang Zhai, Miles J. Efron, Ravishankar Iyer, Michael C. Schatz, Saurabh Sinha, Gene E. Robinson
2015 PLoS Biology  
Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data domains.  ...  We discuss aspects of new technologies that will need to be developed to rise up and meet the computational challenges that genomics poses for the near future.  ...  We would also like to thank all of the participants of the 2014 Keystone Symposium on "Big Data in Biology" (organized by Lincoln D.  ... 
doi:10.1371/journal.pbio.1002195 pmid:26151137 pmcid:PMC4494865 fatcat:mwl4ower4ffgzbaziyqc3tyujq

High-throughput automated microfluidic sample preparation for accurate microbial genomics

Soohong Kim, Joachim De Jonghe, Anthony B. Kulesa, David Feldman, Tommi Vatanen, Roby P. Bhattacharyya, Brittany Berdy, James Gomez, Jill Nolan, Slava Epstein, Paul C. Blainey
2017 Nature Communications  
Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications.  ...  while maintaining or improving data quality.  ...  The indexing barcodes were provided by the Broad Institute Genomics Platform. We also thank Dr Lynn Bry at Brigham and Women's Hospital regarding sample collection and helpful discussions.  ... 
doi:10.1038/ncomms13919 pmid:28128213 pmcid:PMC5290157 fatcat:4psfqq6h6nccpmjzg73plfcnty

Hummingbird: Efficient Performance Prediction for Executing Genomic Applications in the Cloud

Amir Bahmani, Ziye Xing, Vandhana Krishnan, Utsab Ray, Frank Mueller, Amir Alavi, Philip S Tsao, Michael P Snyder, Cuiping Pan, Janet Kelso
2021 Bioinformatics  
Motivation A major drawback of executing genomic applications on cloud computing facilities is the lack of tools to predict which instance type is the most appropriate, often resulting in an over- or under  ...  Results Our experiments on three major genomic data pipelines, including GATK HaplotypeCaller, GATK MuTect2, and ENCODE ATAC-seq, showed that Hummingbird was able to address applications in command line  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Human Genome Research Institute, the National Institutes of Health, or the  ... 
doi:10.1093/bioinformatics/btab161 pmid:33693476 fatcat:sgcbhc3ofjdjtklkbcuqpa7t6e
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