Literature DB >> 32680857

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

Laura Uelze1, Maria Borowiak1, Carlus Deneke1, István Szabó1, Jennie Fischer1, Simon H Tausch1, Burkhard Malorny2.   

Abstract

Keywords:  O antigen; Salmonellazzm321990; serotyping; serovar prediction; whole-genome sequencing

Mesh：

Year:  2020        PMID： 32680857      PMCID： PMC7480391          DOI： 10.1128/AEM.01260-20

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


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  12 in total

1.  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

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

Authors:  Shaoting Li; Shaokang Zhang; Xiangyu Deng
Journal:  Appl Environ Microbiol       Date:  2020-09-01       Impact factor: 4.792

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.  Summarizing and correcting the GC content bias in high-throughput sequencing.

Authors:  Yuval Benjamini; Terence P Speed
Journal:  Nucleic Acids Res       Date:  2012-02-09       Impact factor: 16.971

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.  GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms.

Authors:  Patrick Denis Browne; Tue Kjærgaard Nielsen; Witold Kot; Anni Aggerholm; M Thomas P Gilbert; Lara Puetz; Morten Rasmussen; Athanasios Zervas; Lars Hestbjerg Hansen
Journal:  Gigascience       Date:  2020-02-01       Impact factor: 6.524

9.  Genome-based Salmonella serotyping as the new gold standard.

Authors:  Sangeeta Banerji; Sandra Simon; Andreas Tille; Angelika Fruth; Antje Flieger
Journal:  Sci Rep       Date:  2020-03-09       Impact factor: 4.379

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
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