Literature DB >> 32680856

GC Content-Associated Sequencing Bias Caused by Library Preparation Method May Infrequently Affect Salmonella Serotype Prediction Using SeqSero2.

Shaoting Li1, Shaokang Zhang1, Xiangyu Deng2.   

Abstract

Keywords:  Nextera XT; Salmonellazzm321990; SeqSero2; low GC; sequencing bias; serotype; version control

Mesh：

Year:  2020        PMID： 32680856      PMCID： PMC7480374          DOI： 10.1128/AEM.00614-20

Source DB:  PubMed          Journal:  Appl Environ Microbiol        ISSN： 0099-2240            Impact factor:   4.792


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  10 in total

1.  Library preparation methodology can influence genomic and functional predictions in human microbiome research.

Authors:  Marcus B Jones; Sarah K Highlander; Ericka L Anderson; Weizhong Li; Mark Dayrit; Niels Klitgord; Martin M Fabani; Victor Seguritan; Jessica Green; David T Pride; Shibu Yooseph; William Biggs; Karen E Nelson; J Craig Venter
Journal:  Proc Natl Acad Sci U S A       Date:  2015-10-28       Impact factor: 11.205

2.  Salmonella serotype determination utilizing high-throughput genome sequencing data.

Authors:  Shaokang Zhang; Yanlong Yin; Marcus B Jones; Zhenzhen Zhang; Brooke L Deatherage Kaiser; Blake A Dinsmore; Collette Fitzgerald; Patricia I Fields; Xiangyu Deng
Journal:  J Clin Microbiol       Date:  2015-03-11       Impact factor: 5.948

3.  SeqSero2: Rapid and Improved Salmonella Serotype Determination Using Whole-Genome Sequencing Data.

Authors:  Shaokang Zhang; Hendrik C den Bakker; Shaoting Li; Jessica Chen; Blake A Dinsmore; Charlotte Lane; A C Lauer; Patricia I Fields; Xiangyu Deng
Journal:  Appl Environ Microbiol       Date:  2019-11-14       Impact factor: 4.792

4.  Impact of three Illumina library construction methods on GC bias and HLA genotype calling.

Authors:  James H Lan; Yuxin Yin; Elaine F Reed; Kevin Moua; Kimberly Thomas; Qiuheng Zhang
Journal:  Hum Immunol       Date:  2014-12-25       Impact factor: 2.850

5.  The SPI-3 pathogenicity island of Salmonella enterica.

Authors:  A B Blanc-Potard; F Solomon; J Kayser; E A Groisman
Journal:  J Bacteriol       Date:  1999-02       Impact factor: 3.490

6.  Fishing in the Soup - Pathogen Detection in Food Safety Using Metabarcoding and Metagenomic Sequencing.

Authors:  Josephine Grützke; Burkhard Malorny; Jens Andre Hammerl; Anne Busch; Simon H Tausch; Herbert Tomaso; Carlus Deneke
Journal:  Front Microbiol       Date:  2019-08-06       Impact factor: 5.640

7.  Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes.

Authors:  Mitsuhiko P Sato; Yoshitoshi Ogura; Keiji Nakamura; Ruriko Nishida; Yasuhiro Gotoh; Masahiro Hayashi; Junzo Hisatsune; Motoyuki Sugai; Itoh Takehiko; Tetsuya Hayashi
Journal:  DNA Res       Date:  2019-10-01       Impact factor: 4.458

8.  Lateral transfer and GC content of bacterial resistant genes.

Authors:  Nabil Hayek
Journal:  Front Microbiol       Date:  2013-03-12       Impact factor: 5.640

9.  The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies.

Authors:  Catherine E Yoshida; Peter Kruczkiewicz; Chad R Laing; Erika J Lingohr; Victor P J Gannon; John H E Nash; Eduardo N Taboada
Journal:  PLoS One       Date:  2016-01-22       Impact factor: 3.240

10.  Performance and Accuracy of Four Open-Source Tools for In Silico Serotyping of Salmonella spp. Based on Whole-Genome Short-Read Sequencing Data.

Authors:  Laura Uelze; Maria Borowiak; Carlus Deneke; István Szabó; Jennie Fischer; Simon H Tausch; Burkhard Malorny
Journal:  Appl Environ Microbiol       Date:  2020-02-18       Impact factor: 4.792
  10 in total
  2 in total

1.  Reply to Li et al., "GC Content-Associated Sequencing Bias Caused by Library Preparation Method May Infrequently Affect Salmonella Serotype Prediction Using SeqSero2".

Authors:  Laura Uelze; Maria Borowiak; Carlus Deneke; István Szabó; Jennie Fischer; Simon H Tausch; Burkhard Malorny
Journal:  Appl Environ Microbiol       Date:  2020-09-01       Impact factor: 4.792

2.  Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel.

Authors:  Geneviève Labbé; Peter Kruczkiewicz; James Robertson; Philip Mabon; Justin Schonfeld; Daniel Kein; Marisa A Rankin; Matthew Gopez; Darian Hole; David Son; Natalie Knox; Chad R Laing; Kyrylo Bessonov; Eduardo N Taboada; Catherine Yoshida; Kim Ziebell; Anil Nichani; Roger P Johnson; Gary Van Domselaar; John H E Nash
Journal:  Microb Genom       Date:  2021-09
  2 in total

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