Literature DB >> 27069250

Systematic review of next-generation sequencing simulators: computational tools, features and perspectives.

Min Zhao, Di Liu, Hong Qu.   

Abstract

High-throughput next-generation sequencing (NGS) technologies have rapidly generated a large volume of genomic data. To aid the development and evaluation of new statistical models and computational methods, NGS-based simulators have been proposed to construct better experimental workflows. However, the comparative performance of these NGS simulators remains unclear. In this review, we conducted a comprehensive investigation of NGS simulators for various sequencing techniques, including DNA sequencing, metagenomic sequencing, RNA-seq, ChIP-seq and bisulfite sequencing for methylation.
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Entities:  

Keywords:  high-throughput next-generation sequencing; simulator

Mesh:

Year:  2017        PMID: 27069250     DOI: 10.1093/bfgp/elw012

Source DB:  PubMed          Journal:  Brief Funct Genomics        ISSN: 2041-2649            Impact factor:   4.241


  11 in total

1.  SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data.

Authors:  Tyler Grimes; Somnath Datta
Journal:  J Stat Softw       Date:  2021-07-10       Impact factor: 6.440

2.  Inferring and modeling inheritance of differentially methylated changes across multiple generations.

Authors:  Pascal Belleau; Astrid Deschênes; Marie-Pier Scott-Boyer; Romain Lambrot; Mathieu Dalvai; Sarah Kimmins; Janice Bailey; Arnaud Droit
Journal:  Nucleic Acids Res       Date:  2018-08-21       Impact factor: 16.971

3.  Deduction of Novel Genes Potentially Involved in Osteoblasts of Rheumatoid Arthritis Using Next-Generation Sequencing and Bioinformatic Approaches.

Authors:  Yi-Jen Chen; Wei-An Chang; Ya-Ling Hsu; Chia-Hsin Chen; Po-Lin Kuo
Journal:  Int J Mol Sci       Date:  2017-11-11       Impact factor: 5.923

4.  Identification of novel gene expression signature in lung adenocarcinoma by using next-generation sequencing data and bioinformatics analysis.

Authors:  Ya-Ling Hsu; Jen-Yu Hung; Yen-Lung Lee; Feng-Wei Chen; Kuo-Feng Chang; Wei-An Chang; Ying-Ming Tsai; Inn-Wen Chong; Po-Lin Kuo
Journal:  Oncotarget       Date:  2017-09-18

5.  Identification of novel genetic regulations associated with airway epithelial homeostasis using next-generation sequencing data and bioinformatics approaches.

Authors:  Chau-Chyun Sheu; Ming-Ju Tsai; Feng-Wei Chen; Kuo-Feng Chang; Wei-An Chang; Inn-Wen Chong; Po-Lin Kuo; Ya-Ling Hsu
Journal:  Oncotarget       Date:  2017-07-31

6.  Systematic Analysis of Transcriptomic Profile of Renal Cell Carcinoma under Long-Term Hypoxia Using Next-Generation Sequencing and Bioinformatics.

Authors:  Szu-Chia Chen; Feng-Wei Chen; Ya-Ling Hsu; Po-Lin Kuo
Journal:  Int J Mol Sci       Date:  2017-12-07       Impact factor: 5.923

7.  Identification of novel genes in aging osteoblasts using next-generation sequencing and bioinformatics.

Authors:  Yi-Jen Chen; Wei-An Chang; Ming-Shyan Huang; Chia-Hsin Chen; Kuan-Yuan Wang; Ya-Ling Hsu; Po-Lin Kuo
Journal:  Oncotarget       Date:  2017-11-28

8.  Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing.

Authors:  Marc Noguera-Julian; Emma R Lee; Robert W Shafer; Rami Kantor; Hezhao Ji
Journal:  Viruses       Date:  2020-06-20       Impact factor: 5.818

Review 9.  Discovering myeloid cell heterogeneity in the lung by means of next generation sequencing.

Authors:  Jing-Jing Ji; Jie Fan
Journal:  Mil Med Res       Date:  2019-10-25

10.  Transcriptome Analysis Revealed Inflammation Is Involved in the Impairment of Human Umbilical Vein Endothelial Cells Induced by Post-hemorrhagic Shock Mesenteric Lymph.

Authors:  Qi Wang; Zhen-Fen Chi; Di Wei; Zhen-Ao Zhao; Hong Zhang; Li-Min Zhang; Yan-Xu Liu; An-Ling Kang; Meng Zhao; Peng Wang; Ling-Hu Nie; Chun-Yu Niu; Zi-Gang Zhao
Journal:  Front Immunol       Date:  2020-09-09       Impact factor: 7.561

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