Whole-genome sequencing of A. actinomycetemcomitans

Whole-genome sequencing of the investigated A. actinomycetemcomitans R type isolates and S strains was performed on a Nanopore MinION and Illumina platform. Subsequently, a hybrid assembly of the Nanopore and Illumina sequence data was performed using SPAdes version 3.11 (http://bioinf.spbau.ru/en/content/spades-311-released) (79 (link)). SNP analyses were performed based on short-read sequencing data using Breseq 0.35.7 (80 (link)). The sequence analyses showed that the investigated clinical A. actinomycetemcomitans isolates and their derivative strains lacked extrachromosomal elements, such as plasmids.

Free full text: Click here

Fu Y., Maaβ S., du Teil Espina M., Wolters A.H., Gong Y., de Jong A., Raangs E., Buist G., Westra J., Becher D, & van Dijl J.M. (2022). Connections between Exoproteome Heterogeneity and Virulence in the Oral Pathogen Aggregatibacter actinomycetemcomitans. mSystems, 7(3), e00254-22.

Publication 2022

MinION

Hybrid Plasmids Sequence analyses Strains

Corresponding Organization :

Other organizations : University Medical Center Groningen, University of Groningen, Universität Greifswald, National Institute for Communicable Disease Control and Prevention

Top 5 similar protocols

Variable analysis

independent variables

Whole-genome sequencing of the investigated A. actinomycetemcomitans R type isolates and S strains

dependent variables

SNP analyses based on short-read sequencing data

control variables

Hybrid assembly of the Nanopore and Illumina sequence data using SPAdes version 3.11

controls

No positive or negative controls were explicitly mentioned in the provided information.

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!