Genomic DNA was extracted from isolates using the Qiagen DNeasy kit and protocol (Qiagen, Hilden, Germany). DNA libraries were prepared using Nextera XT (Illumina, San Diego, CA, USA) and whole genome sequencing was performed using the Illumina MiSeq with 2 × 300 bp chemistry. Small Molecular Real Time sequencing was performed on the RS-II (Pacific Biosciences, California, United States) using P6-C4 chemistry, and reference genome assembly was performed as described (Baines et al., 2016 (link)).
Other organizations :
Noguchi Memorial Institute for Medical Research, University of Ghana, Swiss Tropical and Public Health Institute, University of Basel, Peter Doherty Institute, University of Melbourne, Austin Health
Genomic DNA extraction method (Qiagen DNeasy kit and protocol)
DNA library preparation method (Nextera XT)
Whole genome sequencing platform (Illumina MiSeq)
Small Molecular Real Time sequencing platform (Pacific Biosciences RS-II)
dependent variables
Whole genome sequencing data
Reference genome assembly
control variables
Qiagen DNeasy kit and protocol for DNA extraction
Nextera XT for DNA library preparation
Illumina MiSeq 2 × 300 bp chemistry for whole genome sequencing
Pacific Biosciences RS-II with P6-C4 chemistry for Small Molecular Real Time sequencing
Reference genome assembly method as described in Baines et al., 2016
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?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
