Genome Assembly and Comparison Protocol

The total DNA of the genomes was recovered using the EZ1 biorobot (Qiagen, Courtaboeuf, France) and the EZ1 DNA tissue kit. Sequencing was performed using MiSeq technology (Illumina, San Diego, CA, USA) with the Nextera Mate Pair sample prep kit and Nextera XT paired end (Illumina), as previously described (Morel et al. 2015 (link)). Several bioinformatic tools, including Velvet (Zerbino and Birney 2008 (link)), Spades (Bankevich et al. 2012 (link)), and SOAPdenovo (Luo et al. 2012 (link)) were used to assemble the genomes. GapCloser software (Xu et al. 2019 (link)) was used to reduce assembly gaps. Scaffolds which had fewer than 800 base pairs (bp) or had a depth value lower than 25% of the mean depth were removed. The best assembly was selected using different criteria (number of scaffolds, N50, number of N). The degree of genomic similarity of each strain was evaluated by processing sequences using the Orthologous ANI Tool (OAT) software (Lee et al. 2016 (link)). Furthermore, the Genome-to-Genome Distance Calculator (GGDC) web server, which is available online (http://ggdc.dsmz.de), was used to calculate digital DNA–DNA hybridisation (dDDH) values between the genomes of closest species, as previously described (Meier-Kolthoff et al. 2013 (link)).

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Mbaye B., Lo C.I., Dione N., Benabdelkader S., Tidjani Alou M., Brahimi S., Armstrong N., Alibar S., Raoult D., Moal V., Million M., Fournier P.E, & Fenollar F. (2022). Peptoniphilus coli sp. nov. and Peptoniphilus urinae sp. nov., isolated from humans. Archives of Microbiology, 204(8), 506.

Publication 2022

EZ1 biorobot EZ1 DNA tissue kit MiSeq technology Nextera Mate Pair sample prep kit Nextera XT paired end

Genome Genomes hybridisation Strain Tissue Values

Corresponding Organization :

Other organizations : Aix-Marseille Université, Institut de Recherche pour le Développement, Méditerranée Infection Foundation

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Variable analysis

independent variables

Bioinformatic tools used for genome assembly (Velvet, Spades, SOAPdenovo)
GapCloser software used to reduce assembly gaps
Criteria used to select the best genome assembly (number of scaffolds, N50, number of N)

dependent variables

Quality of the genome assemblies (number of scaffolds, N50, number of N)
Degree of genomic similarity between strains (evaluated using Orthologous ANI Tool and Genome-to-Genome Distance Calculator)

control variables

DNA extraction method (EZ1 biorobot and EZ1 DNA tissue kit)
Sequencing technology (MiSeq, Illumina)
Library preparation method (Nextera Mate Pair and Nextera XT paired end)
Scaffold filtering criteria (minimum length 800 bp, minimum depth 25% of mean depth)

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