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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.  ...  fully automated NGS data analysis and sharing in a user-friendly website.  ...  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

RNA-Seq analysis in MeV

E. A. Howe, R. Sinha, D. Schlauch, J. Quackenbush
2011 Bioinformatics  
We also report the addition to MeV of several RNA-Seq-specific functions, addressing the differences in analysis requirements between this data type and traditional gene expression data.  ...  Here, we report a significant enhancement to MeV that allows analysis of RNA-Seq data with these familiar, powerful tools.  ...  ACKNOWLEDGEMENTS We would like to thank the former developers of the MeV and TM4 software projects, as well as the developers of R and Bioconductor.  ... 
doi:10.1093/bioinformatics/btr490 pmid:21976420 pmcid:PMC3208390 fatcat:yv5qcpexe5ezlfcv4rkc3rg4le

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis

Syed Hussain Ather, Olaitan Igbagbo Awe, Thomas J. Butler, Tamiru Denka, Stephen Andrew Semick, Wanhu Tang, Ben Busby
2020 F1000Research  
In conclusion, this well-documented pipeline will introduce state-of-the-art RNA-Seq and ChIP-Seq analysis tools to beginning bioinformaticians and help facilitate the analysis of the burgeoning amounts  ...  To teach interested students and scientists how to analyze RNA-Seq and ChIP-Seq data, we present a start-to-finish tutorial for analyzing RNA-Seq and ChIP-Seq data: SeqAcademy (source code: https://github.com  ...  We would also like to thank the Intramural Research Program of the National Library of Medicine for supporting this work.  ... 
doi:10.12688/f1000research.14880.4 fatcat:wfvx5j5gx5f25k37zsqplgdj6e

Closha: bioinformatics workflow system for the analysis of massive sequencing data

GunHwan Ko, Pan-Gyu Kim, Jongcheol Yoon, Gukhee Han, Seong-Jin Park, Wangho Song, Byungwook Lee
2018 BMC Bioinformatics  
Closha is a hybrid system that enables users to use both analysis programs providing traditional tools and MapReducebased big data analysis programs simultaneously in a single pipeline.  ...  The rapidly increasing amounts of data available from the new high-throughput methods have made data processing infeasible without automated pipelines.  ...  Acknowledgments The authors would like to thank the anonymous reviewers and Closha users for their time and their valuable comments.  ... 
doi:10.1186/s12859-018-2019-3 pmid:29504905 pmcid:PMC5836837 fatcat:6he72saexbbaralajcwfsxgyvu

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis

Syed Hussain Ather, Olaitan Igbagbo Awe, Thomas J. Butler, Tamiru Denka, Stephen Andrew Semick, Wanhu Tang, Ben Busby
2019 F1000Research  
In conclusion, this well-documented pipeline will introduce state-of-the-art RNA-Seq and ChIP-Seq analysis tools to beginning bioinformaticians and help facilitate the analysis of the burgeoning amounts  ...  To teach interested students and scientists how to analyze RNA-Seq and ChIP-Seq data, we present a start-to-finish tutorial for analyzing RNA-Seq and ChIP-Seq data: SeqAcademy (source code: https://github.com  ...  We would also like to thank the Intramural Research Program of the National Library of Medicine for supporting this work.  ... 
doi:10.12688/f1000research.14880.3 fatcat:iqpkzhtr65bcfguohot4nosu5m

SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines

Jérôme Audoux, Mikaël Salson, Christophe F. Grosset, Sacha Beaumeunier, Jean-Marc Holder, Thérèse Commes, Nicolas Philippe
2017 BMC Bioinformatics  
Our SimBA suite of benchmarking tools provides a reliable basis for comparing the performance of RNA-Seq bioinformatics pipelines in addressing a specific biological question.  ...  In order to provide some answers to these questions, we investigate the performance of leading bioinformatic tools designed for RNA-Seq analysis and propose a methodology for systematic evaluation and  ...  Availability of data and materials SimBA software suite as well as the four simulated data-sets and the Snakemake pipeline used to generate the results for this study are freely available at http://cractools.gforge.inria.fr  ... 
doi:10.1186/s12859-017-1831-5 pmid:28969586 pmcid:PMC5623974 fatcat:5c3im544sne5rmxafoz4ozkpoa

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis

Syed Hussain Ather, Olaitan Igbagbo Awe, Thomas J. Butler, Tamiru Denka, Stephen Andrew Semick, Wanhu Tang, Ben Busby
2018 F1000Research  
In conclusion, this well-documented pipeline will introduce state-of-the-art RNA-Seq and ChIP-Seq analysis tools to beginning bioinformaticians and help facilitate the analysis of the burgeoning amounts  ...  To teach interested students and scientists how to analyze RNA-Seq and ChIP-Seq data, we present a start-to-finish tutorial for analyzing RNA-Seq and ChIP-Seq data: SeqAcademy (source code: https://github.com  ...  We would also like to thank the Intramural Research Program of the National Library of Medicine for supporting this work.  ... 
doi:10.12688/f1000research.14880.2 fatcat:6q42rivfrnbahfzmmjjofoxkwu

iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data [article]

Anjana Anilkumar Sithara, Devi Priyanka Maripuri, Keerthika Moorthy, Sai Sruthi Amirtha Ganesh, Philge Philip, Shayantan Banerjee, Malvika Sudhakar, Karthik Raman
2021 bioRxiv   pre-print
Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics.  ...  To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input and outputs insightful statistics on the nature  ...  Acknowledgements The authors acknowledge Mr Likith Reddy for preliminary benchmarking studies and other members of the lab for useful discussions.  ... 
doi:10.1101/2021.09.18.460896 fatcat:yxn7tzf5xjbxlo4mb4vsudlluy

nf-rnaSeqCount: A Nextflow pipeline for obtaining raw read counts from RNA-seq data

Phelelani Mpangase, Jacqueline Frost, Mohammed Tikly, Michèle Ramsay, Scott Hazelhurst
2021 South African Computer Journal  
The aim of this study was to develop a robust portable and reproducible bioinformatic pipeline for the automation of RNA sequencing (RNA-seq) data analyses.  ...  Robust and flexible bioinformatic and computational pipelines for RNA-seq data analysis, from QC to sequence alignment and comparative analyses, will reduce analysis time, and increase accuracy and reproducibility  ...  Ngcungcu for kindly allowing us to use the RNA-seq data on albinism for testing the pipeline.  ... 
doi:10.18489/sacj.v33i2.830 pmid:35574063 pmcid:PMC9097006 fatcat:6uqzuig5frbgtpg7tbr57vvb3e

Computational methods for mapping, assembly and quantification for coding and non-coding transcripts

Isaac A. Babarinde, Yuhao Li, Andrew P. Hutchins
2019 Computational and Structural Biotechnology Journal  
In summary, RNA-Seq is a powerful technology that is likely to remain a key asset in the biologist's toolkit.  ...  In this review, we describe typical computational pipelines for RNA-Seq analysis and discuss their strengths and weaknesses for the assembly, quantification and analysis of coding and non-coding RNAs.  ...  Acknowledgements This work was supported by the National Natural Science Foundation of China (31850410463, 31850410486), Shenzhen Peacock plan, and the Shenzhen Science and Technology Innovation Committee  ... 
doi:10.1016/j.csbj.2019.04.012 pmid:31193391 pmcid:PMC6526290 fatcat:lpfymy2zebc5lf7bs4m356wdzi

Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species

Weizhong Li, R. Alexander Richter, Yunsup Jung, Qiyun Zhu, Robert W. Li
2016 BMC Genomics  
Results: To address the challenges in RNA-seq data analysis, we developed a web portal that offers three integrated workflows that can perform end-to-end compute and analysis, including sequence quality  ...  However, complicated NGS data analysis still remains as a major bottleneck. RNA-seq, as one of the major area in the NGS field, also confronts great challenges in data analysis.  ...  To make sense of RNA-seq data, a full analysis pipeline usually requires multiple procedures and different tools.  ... 
doi:10.1186/s12864-016-3118-z pmid:27678198 pmcid:PMC5039875 fatcat:mrtnh7pgiradhfzu5gw34tkqwm

Unraveling chloroplast transcriptomes with ChloroSeq, an organelle RNA-Seq bioinformatics pipeline

David Roy Smith, Matheus Sanitá Lima
2016 Briefings in Bioinformatics  
The ChloroSeq pipeline uses RNA-Seq alignment data to deliver detailed analyses of organelle transcriptomes, which can be fed into statistical software for further analysis and for generating graphical  ...  Online sequence repositories are teeming with RNA sequencing (RNA-Seq) data from a wide range of eukaryotes.  ...  Once installed, ChloroSeq uses RNA-Seq alignment data (i.e. a BAM file) to deliver a detailed analysis of the plastid transcriptome.  ... 
doi:10.1093/bib/bbw088 pmid:27677960 fatcat:y6anxum4nregjdnxhuv6ptenee

Cloud Computing for Next-Generation Sequencing Data Analysis [chapter]

Shanrong Zhao, Kirk Watrous, Chi Zhang, Baohong Zhang
2017 Cloud Computing - Architecture and Applications  
Genomics studies of large populations are producing a huge amount of data, giving rise to computational issues around the storage, transfer, and analysis of the data.  ...  share the lessons we learned from the implementation of Rainbow, a cloud-based tool for large-scale genome sequencing data analysis.  ...  Similar to DNA sequencing, the enormous data from large-scale RNA-seq studies poses a fundamental challenge for data management and analysis in a local environment [28] [29] [30] .  ... 
doi:10.5772/66732 fatcat:2ewdbtp2bjhx7j7tj4e3auwqke

Orione, a web-based framework for NGS analysis in microbiology

Gianmauro Cuccuru, Massimiliano Orsini, Andrea Pinna, Andrea Sbardellati, Nicola Soranzo, Antonella Travaglione, Paolo Uva, Gianluigi Zanetti, Giorgio Fotia
2014 Computer applications in the biosciences : CABIOS  
End-to-end next-generation sequencing microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics  ...  However, the construction of computational pipelines that use different software packages is difficult owing to a lack of interoperability, reproducibility and transparency.  ...  ACKNOWLEDGEMENTS The authors would like to thank Dr Cesare Camma`(Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise) and Prof. Sergio Uzzau (Universita`di Sassari and Porto Conte  ... 
doi:10.1093/bioinformatics/btu135 pmid:24618473 pmcid:PMC4071203 fatcat:5uopzyti4jalfpwpbpuftks63y

Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology

Donald L. Mykles, Karen G. Burnett, David S. Durica, Blake L. Joyce, Fiona M. McCarthy, Carl J. Schmidt, Jonathon H. Stillman
2016 Integrative and Comparative Biology  
De novo assembly of RNA-seq data has allowed researchers to create a comprehensive catalog of genes expressed in a tissue and to quantify their expression without a complete genome sequence.  ...  The contributions from the "Tapping the Power of Crustacean Transcriptomics to Address Grand Challenges in Comparative Biology" symposium in this issue show the successes and limitations of using RNA-seq  ...  Acknowledgments The authors thank the speakers for their participation in the symposium and Program Officer Sherry Tamone and Burk and Associates staff for their assistance in organizing the symposium  ... 
doi:10.1093/icb/icw083 pmid:27639274 pmcid:PMC5146710 fatcat:j6e67x5ovvhtzdg7aaqkzfvzzy
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