Repository for the Microbiology Resource Announcements paper on several closed Streptococcus suis genomes
We sequenced 5 Streptococcus suis strains using Nanopore MinION sequencing technology. For these strains, Illumina MiSeq data was already available (see accessions.txt for ENA accessions). We assembled complete genomes and characterised these using the Snakemake pipeline provided in this repo.
Snakemake v. 5.7.1 was used to manage the workflow. Please see below for an overview of tools used in which step.
| Process | Tool |
|---|---|
| Downloading Illumina and MinION data | SRA-tools |
| QC and filtering Illumina reads | fastp |
| QC Nanopore reads | FastQC |
| Filtering Nanopore reads | Filtlong |
| Hybrid assembly | Unicycler |
| Assembly QC | Quast |
| MLST calling | mlst |
| Detection resistance genes | ABRicate + NCBI db |
| Detection virulence genes | ABRicate + VFDB db |
| Annotation | Prokka |
| Depth of coverage | Minimap2 + Samtools + BEDtools |
The complete pipeline took ~3.5 hours on a 96GB node using 16 threads.
Five complete genomes were produced, all consisting of a closed chromosome without any extrachromosomal elements. PhiX data was still present in the Illumina data, which gave a second contig in all assemblies. These have been removed from the assemblies uploaded to the ENA. The accessions of the assemblies in ENA are:
| Strain | Genome accession |
|---|---|
| 861160 | GCA_902702745 |
| 9401240 | GCA_902702775 |
| GD-0001 | GCA_902702785 |
| GD-0088 | GCA_902702765 |
| S10 | GCA_902702755 |
The closed genomes were some 40-70kb larger than the short read-only assemblies. We did not identify any regions that were missed in the short read-only assemblies (non-assembling regions?). However, depth of coverage might indicate that several repeats were collapsed in the short read-only assemblies, which caused a difference in size between the hybrid assemblies and the short read-only assemblies.
All data is available from project PRJEB35407.