Whole Genome Sequencing of S. pyogenes

For this study, whole genome sequencing of all clinical isolates (invasive and non-invasive) was performed by the UKHSA reference laboratory using the Illumina NextSeq 1000 platform with 100 base paired-end chemistry. Reads were trimmed to remove adaptor sequences and low-quality bases with Trimmomatic v0.39^{47 (link)}. Contamination was assessed based on Kraken2^{48 (link)} classification of reads mapped against a standard database for bacteria. Genomes with less than 90% of the reads mapped against S. pyogenes were excluded. Draught genomes were generated using SPAdes v3.15.4^{49 (link)}. The assembly quality was assessed using QUAST v5.0.2^{44 (link)}, and poor assemblies were filtered out if the genome size was higher than 2.1 Mbp and/or had more than 400 contigs. Genome annotation was performed with prokka v1.14.6^{46 (link)}.

Free full text: Click here

Vieira A., Wan Y., Ryan Y., Li H.K., Guy R.L., Papangeli M., Huse K.K., Reeves L.C., Soo V.W., Daniel R., Harley A., Broughton K., Dhami C., Ganner M., Ganner M.A., Mumin Z., Razaei M., Rundberg E., Mammadov R., Mills E.A., Sgro V., Mok K.Y., Didelot X., Croucher N.J., Jauneikaite E., Lamagni T., Brown C.S., Coelho J, & Sriskandan S. (2024). Rapid expansion and international spread of M1UK in the post-pandemic UK upsurge of Streptococcus pyogenes. Nature Communications, 15, 3916.

Publication 2024

NextSeq 1000 platform

Corresponding Organization :

Other organizations : Imperial College London, University of Warwick, NIHR Imperial Biomedical Research Centre

Top 5 similar protocols

Variable analysis

independent variables

Whole genome sequencing of all clinical isolates (invasive and non-invasive) was performed by the UKHSA reference laboratory using the Illumina NextSeq 1000 platform with 100 base paired-end chemistry.

dependent variables

Genomes with less than 90% of the reads mapped against S. pyogenes were excluded.
The assembly quality was assessed using QUAST v5.0.2, and poor assemblies were filtered out if the genome size was higher than 2.1 Mbp and/or had more than 400 contigs.

control variables

Reads were trimmed to remove adaptor sequences and low-quality bases with Trimmomatic v0.39.
Contamination was assessed based on Kraken2 classification of reads mapped against a standard database for bacteria.
Draught genomes were generated using SPAdes v3.15.4.
Genome annotation was performed with prokka v1.14.6.

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!