Complete Genome Sequence of Campylobacter armoricus CA639, Which Carries Two Plasmids, Compiled Using Oxford Nanopore and Illumina Sequencing Technologies

被引：2

作者：

Boukerb, Amine M. ^{[1
,3
]}

Schaeffer, Julien ^{[1
]}

Serghine, Joelle ^{[1
]}

Carrier, Gregory ^{[2
]}

Le Guyader, Francoise S. ^{[1
]}

Gourmelon, Michele ^{[1
]}

机构：

[1] Inst Francais Rech Exploitat Mer, Lab Sante Environm & Microbiol, IFREMER RBE SGMM LSEM, Plouzane, France

[2] Inst Francais Rech Exploitat Mer, Lab Physiol & Biotechnol Algues, IFREMER RBE BRM LPBA, Nantes, France

[3] Normandy Univ, Univ Rouen Normandy, Lab Microbiol Signals & Microenvironm LMSM EA4312, Evreux, France

来源：

MICROBIOLOGY RESOURCE ANNOUNCEMENTS | 2020年 / 9卷 / 01期

基金：

欧盟地平线“2020”;

关键词：

READ ALIGNMENT;

D O I：

10.1128/MRA.01309-19

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

As determined by a hybrid approach combining Oxford Nanopore MinION and Illumina MiniSeq sequence data, Campylobacter armoricus strain CA639 harbored a circular chromosome of 1,688,169 bp with a G+C content of 28.47% and two plasmids named pCA639-1 and pCA639-2, with lengths of 51,123 and 28,139 bp, and G+C contents of 26.5% and 28.45%, respectively.

引用

页数：3

共 19 条

[1] SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing [J].

Bankevich, Anton ;

Nurk, Sergey ;

Antipov, Dmitry ;

Gurevich, Alexey A. ;

Dvorkin, Mikhail ;

Kulikov, Alexander S. ;

Lesin, Valery M. ;

Nikolenko, Sergey I. ;

Son Pham ;

Prjibelski, Andrey D. ;

Pyshkin, Alexey V. ;

Sirotkin, Alexander V. ;

Vyahhi, Nikolay ;

Tesler, Glenn ;

Alekseyev, Max A. ;

Pevzner, Pavel A. .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2012, 19 (05) :455-477

[2] Trimmomatic: a flexible trimmer for Illumina sequence data [J].

Bolger, Anthony M. ;

Lohse, Marc ;

Usadel, Bjoern .

BIOINFORMATICS, 2014, 30 (15) :2114-2120

[3] Campylobacter armoricus sp. nov., a novel member of the Campylobacter lari group isolated from surface water and stools from humans with enteric infection [J].

Boukerb, Amine M. ;

Penny, Christian ;

Serghine, Joelle ;

Walczak, Cecile ;

Cauchie, Henry-Michel ;

Miller, William G. ;

Losch, Serge ;

Ragimbeau, Catherine ;

Mossong, Joel ;

Megraud, Francis ;

Lehours, Philippe ;

Benejat, Lucie ;

Gourmelon, Michele .

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2019, 69 (12) :3969-3979

[4] NanoPack: visualizing and processing long-read sequencing data [J].

De Coster, Wouter ;

D'Hert, Svenn ;

Schultz, Darrin T. ;

Cruts, Marc ;

Van Broeckhoven, Christine .

BIOINFORMATICS, 2018, 34 (15) :2666-2669

[5] Assembly of long, error-prone reads using repeat graphs [J].

Kolmogorov, Mikhail ;

Yuan, Jeffrey ;

Lin, Yu ;

Pevzner, Pavel A. .

NATURE BIOTECHNOLOGY, 2019, 37 (05) :540-+

[6] Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation [J].

Koren, Sergey ;

Walenz, Brian P. ;

Berlin, Konstantin ;

Miller, Jason R. ;

Bergman, Nicholas H. ;

Phillippy, Adam M. .

GENOME RESEARCH, 2017, 27 (05) :722-736

[7]

Langmead B, 2012, NAT METHODS, V9, P357, DOI [10.1038/nmeth.1923, 10.1038/NMETH.1923]

[8] Minimap2: pairwise alignment for nucleotide sequences [J].

Li, Heng .

BIOINFORMATICS, 2018, 34 (18) :3094-3100

[9]

Li H, 2009, BIOINFORMATICS, V25, P1754, DOI [10.1093/bioinformatics/btp352, 10.1093/bioinformatics/btp324, 10.1093/bioinformatics/btp698]

[10]

Loman NJ, 2015, NAT METHODS, V12, P733, DOI [10.1038/NMETH.3444, 10.1038/nmeth.3444]

← 1 2 →