SCCion is a genotyping toolkit for Staphylococcus aureus sequence data. It provides three analysis methods:
- fast whole genome typing from assemblies similar to
Kleborate - parallelized read-to-assembly and read-genotyping pipeline in
Nextflow - real-time
MinHashtyping of uncorrected nanopore reads withSketchy
The last component is somewhat experimental, and should be considered a pre-release for now until Sketchy is more mature and has tests and stuff. However, in the few bootstrap analyses we have run on data from S. aureus it performed reasonably well, specifically because we have generated an extensive index of S. aureus genomes from the European Nucleotide Archive for Sketchy. Do not rely on it for more serious matters, like clinical diagnostics. All in all, SCCion combines a variety of databases sourced from many different open-source projects. Please make sure to have a look at the Citations section to see who to pay respect to for their valiant efforts in creating the databases used by SCCion.
Pre-print available on BioRxiv soon.
conda install -c conda-forge -c bioconda -c esteinig sccion
From assembly:
sccion type reference.fasta
From assemblies:
sccion type path/to/assemblies/*.fasta
From uncorrected nanopore reads:
sccion type reads.fq.gz --limit 1000
From uncorrected nanopore reads, live run, watching directory:
sccion type path/to/basecalled/fastq
Nextflow set of paired end reads on default PBS cluster configuration:
nextflow pf-core/pf-sccion -profile cluster --fastq path/to/fastq/*.fq.gz
- Genome assembly typing
- Real-time nanopore typing with
Sketchy - Illumina and ONT read-to-assembly pipelines in
Nextflow
Most importantly, SCCion expects input that is definitely S. aureus or at least a Staphylococcal species (but then SCCmec typing and other genotypes might be off). This is also true for the real-time nanopore typing component, which will break and do all sorts of funky things if input is from species other than S. aureus. One can use a prefiltering step on the reads to make sure this is the case as outlined over at the repository for Sketchy.
SCCion also uses a simple MinHash matching with MASH against the small database of whole SCCmec cassette types collected by the authors of SCCmecFinder. It does not have the rigorous error checking as the original implementation of SCCmecFinder, which should be preferred for subtyping for now.
We rely on a host of excellent software and all too it can go unnoticed when it is wrapped into a program like SCCion. When using SCCion please also cite MASH, SCCmecFinder, Mykrobe, Sketchy, Abricate DBs and refer to the unpublished programs by URL. For specific assembly and typing pipelines, please refer to the tables below.
You can output all citations in RIS format by using:
sccion cite -o sccion_citations
sccion type assembly:
| Program | Author(s) | Publication | Code |
|---|---|---|---|
| MASH | Ondov et al. |  |
 |
| SCCmecFinder | |
|
|
| Mykrobe | |
|
|
| Ridom Spa | Ondov et al. | |
|
| mlst | |
|
|
| Abricate | |
|
|
| Resfinder | Ondov et al. | |
|
| Plasmidfinder | |
|
|
| VFDB | |
|
sccion type nanopore:
| Program | Author(s) | Publication | Code |
|---|---|---|---|
| MASH | Ondov et al. | |
|
| Sketchy | Steinig et al. | |
|
| Nanopath | Steinig | |
|
sccion illumina:
| Program | Author(s) | Publication | Code |
|---|---|---|---|
| Trimmomatic | |
|
|
| Shovill | Seemann et al. | |
|
| Prokka | Seemann | |
|
| Snippy | Seemann et al. | |
|
| SPANDx | Sarovich et al. | |
|
sccion ont:
| Program | Author(s) | Publication | Code |
|---|---|---|---|
| FLYE | |
|
|
| wtdbg2 | |
|
|
| Racon | |
|
|
| Medaka | |
|
|
| Nanopolish | |
|