Streptococcus pyogenes
Usage
The workflow is designed for analyzing of Streptococcus pyogenes.
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
EMM typing
Prediction of virulence factors
Plasmid detection
MLST
cgMLST
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 |
emmtyper |
0.2.0 |
https://depot.galaxyproject.org/singularity/emmtyper:0.2.0–py_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 |
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 |
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 |