Genome assemblies of Staphylococcus pseudintermedius

Supplementary Dataset to the manuscript "Global phylogenomic analysis of Staphylococcus pseudintermedius reveals genomic and prophage diversity in multi-drug resistant lineages", by Lucy F. Grist, Alice Brown, Noel Fitzpatrick, Giuseppina Mariano, Roberto M. La Ragione, Arnoud H. M. van Vliet and Jai W. Mehat.

The dataset contains 2,276 genome assemblies of Staphylococcus pseudintermedius, combining three different types of data, made available here for open research purposes:

Genome assemblies of 110 new UK isolates not previously available. These have also been uploaded into NCBI genome, and have a SCpseud_UoSXXX filename and the SRR code for NCBI SRA.

Genome assemblies (1,144) obtained from the NCBI Genome repository, recognisable by the StaphpseudXXXX_GCA filenames

Genome assemblies (1,022) generated from sequencing reads obtained from NCBI SRA and the ENA repositories, recognisable by the StaphpseudXXXX_SRR and StaphpseudXXXX_ERR filenames.

Genomes were assembled using Shovill version 1.1.0 (https://github.com/tseemann/shovill) using the default settings and the Spades assembler. Only genomes with N50>50 kb, L50<20, and a number of contigs <200 were included in this study.

本补充数据集对应Lucy F. Grist、Alice Brown、Noel Fitzpatrick、Giuseppina Mariano、Roberto M. La Ragione、Arnoud H. M. van Vliet及Jai W. Mehat共同撰写的手稿《中间葡萄球菌（Staphylococcus pseudintermedius）全球系统发育基因组学分析揭示多药耐药谱系的基因组与前噬菌体多样性》。

本数据集包含2276份中间葡萄球菌基因组组装序列，整合三类不同的数据，现面向开放研究公开共享：
1. 110份全新英国分离株的基因组组装序列，此前未对外公开。相关数据已上传至美国国家生物技术信息中心（National Center for Biotechnology Information，NCBI）基因组数据库，文件命名格式为SCpseud_UoSXXX，且对应NCBI序列读取存档（Sequence Read Archive，SRA）的SRR编号。
2. 从NCBI基因组数据库获取的1144份基因组组装序列，文件名以StaphpseudXXXX_GCA为标识。
3. 从NCBI SRA及欧洲核苷酸档案馆（European Nucleotide Archive，ENA）数据库的测序reads中组装得到的1022份基因组组装序列，文件名以StaphpseudXXXX_SRR及StaphpseudXXXX_ERR为标识。

所有基因组均使用Shovill 1.1.0版本（https://github.com/tseemann/shovill），以默认参数结合Spades组装器完成组装。本研究仅纳入N50>50 kb、L50<20且重叠群（contig）数量<200的基因组序列。