Literature DB >> 26519411

Tablet: Visualizing Next-Generation Sequence Assemblies and Mappings.

Iain Milne1, Micha Bayer2, Gordon Stephen2, Linda Cardle2, David Marshall2.   

Abstract

This chapter is designed to be a practical guide to using Tablet for the visualization of next/second-generation (NGS) sequencing data. NGS data is being produced more frequently and in greater data volumes every year. As such, it is increasingly important to have tools which enable biologists and bioinformaticians to understand and gain key insights into their data. Visualization can play a key role in the exploration of such data as well as aid in the visual validation of sequence assemblies and features such as single nucleotide polymorphisms (SNPs). We aim to show several use cases which demonstrate Tablet's ability to visually highlight various situations of interest which can arise in NGS data.

Keywords:  Assembly; Mapping; Next-generation sequencing; SNP discovery; Visualization

Mesh:

Year:  2016        PMID: 26519411     DOI: 10.1007/978-1-4939-3167-5_14

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


  22 in total

1.  Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture.

Authors:  Kristine M Wylie; Todd N Wylie; Richard Buller; Brandi Herter; Maria T Cannella; Gregory A Storch
Journal:  J Clin Microbiol       Date:  2018-11-27       Impact factor: 5.948

2.  Potent neuroprotection after stroke afforded by a double-knot spider-venom peptide that inhibits acid-sensing ion channel 1a.

Authors:  Irène R Chassagnon; Claudia A McCarthy; Yanni K-Y Chin; Sandy S Pineda; Angelo Keramidas; Mehdi Mobli; Vi Pham; T Michael De Silva; Joseph W Lynch; Robert E Widdop; Lachlan D Rash; Glenn F King
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-20       Impact factor: 11.205

Review 3.  Going the Distance: Optimizing RNA-Seq Strategies for Transcriptomic Analysis of Complex Viral Genomes.

Authors:  Daniel P Depledge; Ian Mohr; Angus C Wilson
Journal:  J Virol       Date:  2018-12-10       Impact factor: 5.103

4.  Evolutionary pathway analysis and unified classification of East Asian lineage of Mycobacterium tuberculosis.

Authors:  Egor Shitikov; Sergey Kolchenko; Igor Mokrousov; Julia Bespyatykh; Dmitry Ischenko; Elena Ilina; Vadim Govorun
Journal:  Sci Rep       Date:  2017-08-23       Impact factor: 4.379

5.  NOVOPlasty: de novo assembly of organelle genomes from whole genome data.

Authors:  Nicolas Dierckxsens; Patrick Mardulyn; Guillaume Smits
Journal:  Nucleic Acids Res       Date:  2017-02-28       Impact factor: 16.971

6.  Whole-Genome Sequencing of Klebsiella pneumoniae Isolates to Track Strain Progression in a Single Patient With Recurrent Urinary Tract Infection.

Authors:  Kristine M Wylie; Todd N Wylie; Patrick J Minx; David A Rosen
Journal:  Front Cell Infect Microbiol       Date:  2019-02-08       Impact factor: 5.293

7.  Genetic Evaluation of Nosocomial Candida auris Transmission.

Authors:  Egon A Ozer; Chao Qi; Scott C Roberts; Teresa R Zembower
Journal:  J Clin Microbiol       Date:  2021-03-19       Impact factor: 5.948

8.  Reversible gene silencing through frameshift indels and frameshift scars provide adaptive plasticity for Mycobacterium tuberculosis.

Authors:  Aditi Gupta; David Alland
Journal:  Nat Commun       Date:  2021-08-04       Impact factor: 14.919

9.  Highly Pathogenic Clone of Shiga Toxin-Producing Escherichia coli O157:H7, England and Wales.

Authors:  Lisa Byrne; Timothy J Dallman; Natalie Adams; Amy F W Mikhail; Noel McCarthy; Claire Jenkins
Journal:  Emerg Infect Dis       Date:  2018-12       Impact factor: 6.883

10.  BioSankey: Visualization of Microbial Communities Over Time.

Authors:  Alexander Platzer; Julia Polzin; Klaus Rembart; Ping Penny Han; Denise Rauer; Thomas Nussbaumer
Journal:  J Integr Bioinform       Date:  2018-06-13
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