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Literature DB >> 24743989

Analysis of next-generation sequencing data using Galaxy.

Daniel Blankenberg¹, Jennifer Hillman-Jackson.

Abstract

The extraordinary throughput of next-generation sequencing (NGS) technology is outpacing our ability to analyze and interpret the data. This chapter will focus on practical informatics methods, strategies, and software tools for transforming NGS data into usable information through the use of a web-based platform, Galaxy. The Galaxy interface is explored through several different types of example analyses. Instructions for running one's own Galaxy server on local hardware or on cloud computing resources are provided. Installing new tools into a personal Galaxy instance is also demonstrated.

Mesh：

Year: 2014 PMID： 24743989 DOI： 10.1007/978-1-4939-0512-6_2

Source DB: PubMed Journal: Methods Mol Biol ISSN： 1064-3745

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Cited

16 in total

1. Global Tn-seq analysis of carbohydrate utilization and vertebrate infectivity of Borrelia burgdorferi.

Authors: Erin B Troy; Tao Lin; Lihui Gao; David W Lazinski; Maureen Lundt; Andrew Camilli; Steven J Norris; Linden T Hu
Journal: Mol Microbiol Date: 2016-07-15 Impact factor: 3.501

2. FAST: FAST Analysis of Sequences Toolbox.

Authors: Travis J Lawrence; Kyle T Kauffman; Katherine C H Amrine; Dana L Carper; Raymond S Lee; Peter J Becich; Claudia J Canales; David H Ardell
Journal: Front Genet Date: 2015-05-19 Impact factor: 4.599

3. High-Throughput Quantification of In Vivo Adeno-Associated Virus Transduction with Barcoded Non-Coding RNAs.

Authors: Meiyu Xu; Jia Li; Jun Xie; Ran He; Qin Su; Guangping Gao; Phillip W L Tai
Journal: Hum Gene Ther Date: 2019-06-17 Impact factor: 5.695

4. Male bovine GH transgenic mice have decreased adiposity with an adipose depot-specific increase in immune cell populations.

Authors: Fabian Benencia; Stephanie Harshman; Silvana Duran-Ortiz; Ellen R Lubbers; Edward O List; Lara Householder; Mawadda Al-Naeeli; Xiaoyu Liang; Lonnie Welch; John J Kopchick; Darlene E Berryman
Journal: Endocrinology Date: 2014-12-18 Impact factor: 4.736

5. An integrative network analysis framework for identifying molecular functions in complex disorders examining major depressive disorder as a test case.

Authors: Anup Mammen Oommen; Stephen Cunningham; Páraic S O'Súilleabháin; Brian M Hughes; Lokesh Joshi
Journal: Sci Rep Date: 2021-05-06 Impact factor: 4.379

Analysis of next-generation sequencing data using Galaxy.

1. Global Tn-seq analysis of carbohydrate utilization and vertebrate infectivity of Borrelia burgdorferi.

2. FAST: FAST Analysis of Sequences Toolbox.

3. High-Throughput Quantification of In Vivo Adeno-Associated Virus Transduction with Barcoded Non-Coding RNAs.

4. Male bovine GH transgenic mice have decreased adiposity with an adipose depot-specific increase in immune cell populations.

5. An integrative network analysis framework for identifying molecular functions in complex disorders examining major depressive disorder as a test case.

6. Subgingival microbiota in health compared to periodontitis and the influence of smoking.

7. A DNA methylation-based liquid biopsy for triple-negative breast cancer.

8. The Notch-mediated hyperplasia circuitry in Drosophila reveals a Src-JNK signaling axis.

9. Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework.

10. TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation.