Escherichia coli
Usage
The workflow is designed for analysis of Escherichia coli (including ETEC, EIEC, and EPEC) and Shigella spp.
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
STX typing
Serotyping
Discrimination between ETEC, EIEC, EPEC, and Shigella
MLST
cgMLST
Software & database 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 |
seqtk |
1.4 |
https://depot.galaxyproject.org/singularity/seqtk:1.4–he4a0461_2 |
serotypefinder |
2.0.2 |
https://depot.galaxyproject.org/singularity/serotypefinder:2.0.2–py312hdfd78af_1 |
serotypefinder_db |
ada62c62a7fa74032448bb2273d1f7045c59fdda |
https://depot.galaxyproject.org/singularity/serotypefinder:2.0.2–py312hdfd78af_1 |
shigatyper |
2.0.5 |
https://depot.galaxyproject.org/singularity/shigatyper:2.0.5–pyhdfd78af_0 |
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 |