Staphylococcus aureus
Usage
The workflow is designed for analyzing of Staphylococcus aureus.
Supported analysis
The workflow includes the following analysis in addition to species prediction and various methods for assessing the sequencing quality,
Antibiotic resistance prediction
Disinfectant resistance
Prediction of virulence factors
Plasmid detection
MLST
cgMLST
SCCmec type
spa type (for ONT workflow)
Software versions
Software |
Version |
Container |
amrfinderplus |
4.2.7 |
https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:4.2.7–hf69ffd2_0 |
bracken |
2.8 |
https://depot.galaxyproject.org/singularity/bracken:2.8–py39hc16433a_0 |
bwa |
0.7.17-r1188 |
https://depot.galaxyproject.org/singularity/bwakit:0.7.17.dev1–hdfd78af_1 |
chewbbaca |
3.5.3 |
https://depot.galaxyproject.org/singularity/chewbbaca:3.5.3–pyh106432d_1 |
clair3 |
2.0.0 |
docker://hkubal/clair3:v2.0.0 |
fastqc |
0.12.1 |
https://depot.galaxyproject.org/singularity/fastqc:0.12.1–hdfd78af_0 |
filtlong |
0.3.1 |
https://depot.galaxyproject.org/singularity/filtlong:0.3.1–h077b44d_0 |
flye |
2.9.6 |
https://depot.galaxyproject.org/singularity/flye:2.9.6–py39h475c85d_0 |
freebayes |
1.3.6 |
https://depot.galaxyproject.org/singularity/freebayes:1.3.6–hbfe0e7f_2 |
hostile |
2.0.0 |
https://depot.galaxyproject.org/singularity/hostile:2.0.0–pyhdfd78af_0 |
kraken2 |
2.17.1 |
https://depot.galaxyproject.org/singularity/mulled-v2-f8c4015c836dd3ce5c118cfed97ec8259bab9e9d:41404a18634d1ec6fe2a8a0dc54df6925d57fdbf-0 |
minimiap2 |
2.30 |
https://depot.galaxyproject.org/singularity/minimap2:2.30–h577a1d6_0 |
medaka |
2.2.0 |
docker://ontresearch/medaka:shacf8338462607b17b1d68dbce212cb93daea50bad |
mlst |
2.23.0 |
https://depot.galaxyproject.org/singularity/mlst:2.23.0–hdfd78af_1 |
nanoplot |
1.46.2 |
https://depot.galaxyproject.org/singularity/nanoplot:1.46.2–pyhdfd78af_0 |
plasmidfinder |
2.1.6 |
https://depot.galaxyproject.org/singularity/plasmidfinder:2.1.6–py314hdfd78af_2 |
pointfinder_db |
4.0.0 |
https://depot.galaxyproject.org/singularity/resfinder:4.4.2–pyhdfd78af_1 |
prp |
1.6.1 |
docker://clinicalgenomicslund/bonsai-prp:1.6.1 |
quast |
5.2.0 |
https://depot.galaxyproject.org/singularity/quast:5.2.0–py310pl5321hc8f18ef_2 |
resfinder |
4.4.2 |
https://depot.galaxyproject.org/singularity/resfinder:4.4.2–pyhdfd78af_1 |
resfinder_db |
2.1.1 |
https://depot.galaxyproject.org/singularity/resfinder:4.4.2–pyhdfd78af_1 |
samtools |
1.17 |
https://depot.galaxyproject.org/singularity/samtools:1.17–h00cdaf9_0 |
sccmec |
1.2.0 |
https://depot.galaxyproject.org/singularity/sccmec:1.2.0–hdfd78af_0 |
seqtk |
1.4 |
https://depot.galaxyproject.org/singularity/seqtk:1.4–he4a0461_2 |
ska2 |
0.3.10 |
https://depot.galaxyproject.org/singularity/ska2:0.3.10–h4349ce8_0 |
skesa |
2.5.1 |
https://depot.galaxyproject.org/singularity/skesa:2.5.1–hdcf5f25_0 |
sourmash |
4.8.2 |
https://depot.galaxyproject.org/singularity/sourmash:4.8.2–hdfd78af_0 |
spades |
3.15.5 |
https://depot.galaxyproject.org/singularity/spades:3.15.5–h95f258a_1 |
spatyper |
0.3.3 |
https://depot.galaxyproject.org/singularity/spatyper:0.3.3–pyhdfd78af_3 |
trimmomatic |
0.40 |
https://depot.galaxyproject.org/singularity/trimmomatic:0.40–hdfd78af_0 |
virulencefinder |
2.0.4 |
https://depot.galaxyproject.org/singularity/virulencefinder:2.0.4–hdfd78af_1 |
virulencefinder_db |
041b8b30ede055f92cbd8eaf3679ca7554857514 |
https://depot.galaxyproject.org/singularity/virulencefinder:2.0.4–hdfd78af_1 |