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Manipulation of FASTQ data with Galaxy

D. Blankenberg, A. Gordon, G. Von Kuster, N. Coraor, J. Taylor, A. Nekrutenko
2010 Bioinformatics  
Here, we describe a tool suite that functions on all of the commonly known FASTQ format variants and provides a pipeline for manipulating next generation sequencing data taken from a sequencing machine  ...  Availability and Implementation: This open-source toolset was implemented in Python and has been integrated into the online data analysis platform Galaxy (public web access: http://usegalaxy.org; download  ...  with Galaxy.  ... 
doi:10.1093/bioinformatics/btq281 pmid:20562416 pmcid:PMC2894519 fatcat:xyipiqidw5hcze2okkkguhefdi

Tutorial : Resolution of a clinical case from a data set [article]

Guillaume Gricourt
2020 Zenodo  
Master 2 : Biology Healthcare UE : The diagnosis in infectious diseases and its development Lesson : "Tutorial : Resolution of a clinical case from a data set"  ...  our data, FASTQ, to Galaxy.  ...  Introduction Pipeline analysis Overview of all steps we will perform : Load data First of all, we need to login into Galaxy.  ... 
doi:10.5281/zenodo.4249194 fatcat:35724z3osrgsndzj3mnnddum5u

Analyzing HT-SELEX data with the Galaxy Project tools – A web based bioinformatics platform for biomedical research

William H. Thiel, Paloma H. Giangrande
2016 Methods  
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ...  ACKNOWLEDGMENTS This work was supported by the American Heart Association (11POST7620018, 13POST17070101, and 14SDG18850071 to WHT), the National Institutes of Health (R01CA138503 and R21DE019953 to PHG  ...  The NGS: QC and manipulation\FASTQ Groomer tool may be necessary to first convert the FASTQ data file to a format that the NGS: QC and manipulation\Filter by quality tool recognizes.  ... 
doi:10.1016/j.ymeth.2015.10.008 pmid:26481156 pmcid:PMC4792767 fatcat:rnwjqfejobaytl3qrc4aw7m2ee

Methods for analyzing next-generation sequencing data XI.Galaxy -an integrated data analysis environment

Tazro Ohta, Tomoko Terada, Kentaro Shimizu, Koji Kadota
2017 Japanese Journal of Lactic Acid Bacteria  
本稿で紹介する Galaxy 2-5) は、GUI 環境で解析を行う ための便利な手段という位置づけとなる。連載第 1 回 6) で も述べたように、バイオインフォマティクス中級~上級を 目指す場合には、NGS ハンズオン講習会の受講資格でも ある Linux 環境構築や基本的な Linux コマンドの習得が 最低限の心得であろう。  ...  Genome Res 15: 1451-1455. 3) Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, et al. (2010) Manipulation of FASTQ data with Galaxy.  ...  ルとプログラムのインストール.日本乳酸菌学会誌 26: 124-132. 13) Lo CC, Chain PS. (2014) Rapid evaluation and quality control of next generation sequencing data with FaQCs.  ... 
doi:10.4109/jslab.28.167 fatcat:4c3ac4445verplvo3usmgoxgny

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework

Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø Arntzen, Benoit J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson (+2 others)
2021 F1000Research  
In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform.  ...  characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.  ...  Grüning (University of Freiburg, Germany) for helping us during the implementation of the workflow in the European Galaxy platform.  ... 
doi:10.12688/f1000research.28608.2 fatcat:yuuo6xirpfh6voh7d2iqve7bzm

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE

Quang M Trinh, Fei-Yang Jen, Ziru Zhou, Kar Chu, Marc D Perry, Ellen T Kephart, Sergio Contrino, Peter Ruzanov, Lincoln D Stein
2013 BMC Genomics  
modifications and enhancements of the original protocols, or combine modENCODE data with other data sets.  ...  With a total size of just under 10 terabytes of data collected and released to the public, one of the challenges faced by researchers is to extract biologically meaningful knowledge from this large data  ...  Implementation The modENCODE DCC provides public access to the modENCODE data set in a variety of formats, and is also charged with releasing convenient tools for manipulating the data.  ... 
doi:10.1186/1471-2164-14-494 pmid:23875683 pmcid:PMC3734164 fatcat:x5a4eoozb5eqdczxq7cy6ycgiq

Galaxy Workflows for Web-based Bioinformatics Analysis of Aptamer High-throughput Sequencing Data

William H Thiel
2016 Molecular Therapy: Nucleic Acids  
Using a series of Workflows created in the Galaxy webserver, we demonstrate efficient processing of aptamer HTS data and compilation of a database of unique aptamer sequences.  ...  A key advantage of this approach is that the online nature of the Galaxy webserver and its graphical interface allow for the analysis of HTS data without the need to compile code or install multiple programs  ...  The funders had no role in the design of the study, collection and analysis of the data, or the decision to publish. We thank Paloma H. Giangrande, George J. Weiner, Suresh Veeramani, Sue E.  ... 
doi:10.1038/mtna.2016.54 pmid:28131286 pmcid:PMC5023399 fatcat:vlxiphpfkvf4bllqk37kjgbtqe

I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples

Zeeshan Ahmed, Duygu Ucar
2017 PeerJ  
Thus, the barrier to deriving important clinical insights from clinical epigenomic samples is no longer one of data generation but of data analysis.  ...  Its performance has been tested using public ATAC-seq datasets in GM12878 and CD4+T cells and a feature-based comparison is performed with some available interactive LIMS (Galaxy, SMITH, SeqBench, Wasp  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.7717/peerj.4040 pmid:29181276 pmcid:PMC5702251 fatcat:4yi664uqezhq7ht6mgga2o5uzy

Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system

Todd H Oakley, Markos A Alexandrou, Roger Ngo, M Pankey, Celia K C Churchill, William Chen, Karl B Lopker
2014 BMC Bioinformatics  
Osiris enables all aspects of phylogenetic analysis within Galaxy, including de novo assembly of high throughput sequencing reads, ortholog identification, multiple sequence alignment, concatenation, phylogenetic  ...  Results: We developed a suite of wrappers for new and existing phylogenetics tools for the Galaxy workflow management system that we call Osiris.  ...  SFF TO FASTA & QUAL*FASTQ TO FASTA* SRA TO FASTQ* FASTA OR TABULAR FASTQ & SFF QUALITY CONTROL & CONVERSION NGS QC & MANIPULATION GALAXY* ILLUQC* SCYTHE* TAGDUST* TRIMMING READS* FORMAT CONVERSION  ... 
doi:10.1186/1471-2105-15-230 pmid:24990571 pmcid:PMC4227113 fatcat:stzllhl2zzh3znlpinrafnwxea

Online Resources for Genomic Analysis Using High-Throughput Sequencing

Daniel Blankenberg, James Taylor, Anton Nekrutenko
2015 Cold Spring Harbor Protocols  
As a consequence, several online resources and communities have been developed to assist researchers with both the management and the analysis of sequencing data sets.  ...  , and provide examples of typical analyses with links to further detailed exercises.  ...  ACKNOWLEDGMENTS We, the investigators of this introduction, are lead members of the Galaxy Project team. We thank the other members of the Galaxy Team (E. Afgan, D. Baker, D.B., D. Bouvier, M.  ... 
doi:10.1101/pdb.top083667 pmid:25655493 fatcat:ooet5nofajciro52qzauyo25ka

GTO: a toolkit to unify pipelines in genomic and proteomic research [article]

Joao Rafael Almeida, Armando J Pinho, José Luis Oliveira, Olga Fajarda, Diogo Pratas
2020 biorxiv/medrxiv   pre-print
Next-generation sequencing triggered the production of a massive volume of publicly available data and the development of new specialised tools.  ...  the data.  ...  NETDIAMOND, Portugal project (POCI-01-0145-FEDER-016385), co-funded by Centro 2020 program, Portugal 2020, European Union, and from the FCT -Foundation for Science and Technology, Portugal, in the context of  ... 
doi:10.1101/2020.01.07.882845 fatcat:xcc26ffahnbhpfq74ww7wqoo6i

ASaiM: a Galaxy-based framework to analyze raw shotgun data from microbiota [article]

Bérénice Batut, Kévin Gravouil, Clémence Defois, Saskia Hiltemann, Jean-François Brugère, Eric Peyretaillade, Pierre Peyret
2017 bioRxiv   pre-print
We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses.  ...  ASaiM provides a powerful framework to easily and quickly explore microbiota data in a reproducible and transparent environment.  ...  Galaxy ToolShed BAM/SAM file manipulation SAM tools [15-17] BIOM file manipulation BIOM-Format tools [18] Genomics tools Assembly FastQ joiner [19] , FastQ-join Quality control FastQC, PRINSEQ  ... 
doi:10.1101/183970 fatcat:ibolunrhlzc4nldbpj2pbof56m

A case study for cloud based high throughput analysis of NGS data using the globus genomics system

Krithika Bhuvaneshwar, Dinanath Sulakhe, Robinder Gauba, Alex Rodriguez, Ravi Madduri, Utpal Dave, Lukasz Lacinski, Ian Foster, Yuriy Gusev, Subha Madhavan
2015 Computational and Structural Biotechnology Journal  
We present a case study of a practical solution to this data management and analysis challenge that simplifies terabyte scale data handling and provides advanced tools for NGS data analysis.  ...  These capabilities are implemented using the "Globus Genomics" system, which is an enhanced Galaxy workflow system made available as a service that offers users the capability to process and transfer data  ...  Although Galaxy is easy to use, it has data upload, storage and data manipulation bottlenecks, especially for large datasets.  ... 
doi:10.1016/j.csbj.2014.11.001 pmid:26925205 pmcid:PMC4720014 fatcat:ca7nkznpnjafjcgxtcghst5flm

Visual programming for next-generation sequencing data analytics

Franco Milicchio, Rebecca Rose, Jiang Bian, Jae Min, Mattia Prosperi
2016 BioData Mining  
Although a plethora of tools for NGS data analysis has emerged in the past decade, (i) software development is still lagging behind data generation capabilities, and (ii) there is a 'cultural' gap between  ...  Processing and analyzing NGS data is challenging. NGS data are big, heterogeneous, sparse, and error prone.  ...  design of new ones with its built-in workflow builder, as in Galaxy (with similar limitations).  ... 
doi:10.1186/s13040-016-0095-3 pmid:27127540 pmcid:PMC4848821 fatcat:tvbjlx36hbgblb5x5dl7tah6fe

Extending KNIME for next-generation sequencing data analysis

Bernd Jagla, Bernd Wiswedel, Jean-Yves Coppée
2011 Computer applications in the biosciences : CABIOS  
KNIME (Konstanz Information Miner) is a user-friendly and comprehensive open-source data integration, processing, analysis, and exploration platform.  ...  ACKNOWLEDGEMENTS We thank Odile Sismeiro and Caroline Proux for helpful discussions and testing of the workflows. We thank Dr. Kenneth Smith for critical reading of the manuscript.  ...  The purpose of these workflows is to provide new users with some examples of data handling and provide a good starting point for fast data generation.  ... 
doi:10.1093/bioinformatics/btr478 pmid:21873641 fatcat:gx42ua6c7ngkdmpr5epq7wocga
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