Sequencing data and assembled genomes of bacteria isolated from seafood products (ANR SEABIOMIC)
Twelve phylogenetically distant bacteria from seafood product were sequenced using Oxford Nanopore (R9.4 chemistry; MinION MK1C; 3 different libraries preparation) and Illumina (NextSeq system) technologies. These reference genomes were used to assess popular assembly tools to complete circular replicons (chromosomes and plasmids) and examine sequencing perfomance (Sauvage et al., 2023, submitted).
Simple
- Title
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Sequencing data and assembled genomes of bacteria isolated from seafood products (ANR SEABIOMIC)
- Date (Creation)
- 2022-06-01
- Date (Publication)
- 2023-05-05
- Citation identifier
- FR-330-715-368-00032-IFR_BIOINFO_WGS_SEABIOMIC
- Abstract
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Twelve phylogenetically distant bacteria from seafood product were sequenced using Oxford Nanopore (R9.4 chemistry; MinION MK1C; 3 different libraries preparation) and Illumina (NextSeq system) technologies. These reference genomes were used to assess popular assembly tools to complete circular replicons (chromosomes and plasmids) and examine sequencing perfomance (Sauvage et al., 2023, submitted).
- Credit
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Ifremer - Laboratoire RBE/MASAE/EM3B
- Point of contact
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Organisation name Individual name Electronic mail address Role IFREMER
Publisher IFREMER
Sauvage Thomas
Author IFREMER
Cormier Alexandre
Author IFREMER
Passerini Delphine
Author
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Thèmes Sextant
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/Biological Environment/Bioinformatics
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GEMET - INSPIRE themes, version 1.0
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Habitats and biotopes
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ODATIS aggregation parameters and Essential Variable names
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Bioinformatics
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- Use limitation
- CC-BY (Creative Commons - Attribution)
- Access constraints
- License
- Use constraints
- License
- Spatial representation type
- Vector
- Language
- English
- Character set
- UTF8
- Topic category
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- Oceans
- Distribution format
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Name Version
- OnLine resource
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Protocol Linkage Name NETWORK:LINK
/home/ref-bioinfo-public/ifremer/brm/seabiomic WWW:DOWNLOAD
https://data-dataref.ifremer.fr/bioinfo/ifremer/brm/seabiomic/ Download link
- OnLine resource
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Protocol Linkage Name DOI
https://doi.org/10.12770/752b03c1-06bf-4c0b-93c6-0f14b28297b0 Digital Object Identifier (DOI)
- Hierarchy level
- Dataset
Conformance result
- Title
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RÈGLEMENT (UE) N o 1089/2010 DE LA COMMISSION du 23 novembre 2010 portant modalités d'application de la directive 2007/2/CE du Parlement européen et du Conseil en ce qui concerne l'interopérabilité des séries et des services de données géographiques
- Date (Publication)
- 2010-12-08
- Explanation
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See the referenced specification
- Pass
- Statement
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Twelve seafood bacteria from Ifremer-MASAE-EM3B collection (strains CD3406, MIP2602, SF1671, EBP3064, HIS2824, SF2022, MIP2422, SAF3325, MIP2461, SAF3333, MIP2473, SF1039) were sequenced using Oxford Nanopore (R9.4 chemistry; MinION MK1C) and Illumina (NextSeq system) technologies. The effect of ONT’s library preparation strategies was assessed on the sequencing accuracy and assembly quality of these 12 genomes. Three libraries including barcode attachment via tagmentation (TAG), via ligation (LIG) or via PCR amplification (PCR) were compared.
Downloadable files include:
-Illumina raw sequences (.fastq) for 12 bacterial strains
-Nanopore raw sequences (.fast5, .fastq) following the 3 library preparations for 12 bacterial strains
-Genome assemblies including chromosomes and plasmids (.fasta)
-Reports of reads and tandem repeat properties.
This work was supported by the French Agency for Research (Agence Nationale de la Recherche) grant number ANR-20-CE21-0001-01 (SEABIOMIC project).
Metadata
- File identifier
- 752b03c1-06bf-4c0b-93c6-0f14b28297b0
- Metadata language
- English
- Character set
- UTF8
- Hierarchy level
- Dataset
- Date stamp
- 2023-06-13T12:43:03.486Z
- Metadata standard name
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ISO 19115:2003/19139 - SEXTANT
- Metadata standard version
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1.0
- Metadata author
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Organisation name Individual name Electronic mail address Role IFREMER
Passerini Delphine
Local service desk
