Main tool: ectyper
Code repository: https://github.com/phac-nml/ecoli_serotyping
Additional tools installed via micromamba:
Name Version Build Channel
────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bcftools 1.21 h3a4d415_1 bioconda
biopython 1.85 py313h536fd9c_1 conda-forge
blast 2.16.0 h66d330f_5 bioconda
bowtie2 2.5.4 he96a11b_5 bioconda
brotli-python 1.1.0 py313h46c70d0_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.4.26 hbd8a1cb_0 conda-forge
capnproto 1.0.2 h766bdaa_3 conda-forge
certifi 2025.4.26 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py313hfab6e84_0 conda-forge
charset-normalizer 3.4.2 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
curl 8.14.0 h332b0f4_0 conda-forge
ectyper 2.0.0 pyhdfd78af_4 bioconda
entrez-direct 22.4 he881be0_0 bioconda
exceptiongroup 1.3.0 pyhd8ed1ab_0 conda-forge
gsl 2.7 he838d99_0 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
htslib 1.21 h566b1c6_1 bioconda
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
iniconfig 2.0.0 pyhd8ed1ab_1 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
libasprintf 0.24.1 h8e693c7_0 conda-forge
libblas 3.9.0 31_h59b9bed_openblas conda-forge
libcblas 3.9.0 31_he106b2a_openblas conda-forge
libcurl 8.14.0 h332b0f4_0 conda-forge
libdeflate 1.24 h86f0d12_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.0 h5888daf_0 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libgcc 15.1.0 h767d61c_2 conda-forge
libgcc-ng 15.1.0 h69a702a_2 conda-forge
libgettextpo 0.24.1 h5888daf_0 conda-forge
libgfortran 15.1.0 h69a702a_2 conda-forge
libgfortran5 15.1.0 hcea5267_2 conda-forge
libgomp 15.1.0 h767d61c_2 conda-forge
libidn2 2.3.8 ha4ef2c3_0 conda-forge
liblapack 3.9.0 31_h7ac8fdf_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_1 conda-forge
libmpdec 4.0.0 hb9d3cd8_0 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libopenblas 0.3.29 pthreads_h94d23a6_0 conda-forge
libsqlite 3.49.2 hee588c1_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.1.0 h8f9b012_2 conda-forge
libstdcxx-ng 15.1.0 h4852527_2 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
mash 2.3 hb105d93_9 bioconda
ncbi-vdb 3.2.1 h9948957_0 bioconda
ncurses 6.5 h2d0b736_3 conda-forge
numpy 2.2.6 py313h17eae1a_0 conda-forge
openssl 3.5.0 h7b32b05_1 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.2.3 py313ha87cce1_3 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-common-sense 3.75 pl5321hd8ed1ab_0 conda-forge
perl-compress-raw-bzip2 2.201 pl5321hbf60520_1 conda-forge
perl-compress-raw-zlib 2.202 pl5321hadc24fc_0 conda-forge
perl-encode 3.21 pl5321hb9d3cd8_1 conda-forge
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0 conda-forge
perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge
perl-io-compress 2.201 pl5321h503566f_5 bioconda
perl-io-zlib 1.14 pl5321hdfd78af_0 bioconda
perl-json 4.10 pl5321hdfd78af_1 bioconda
perl-json-xs 4.03 pl5321h9948957_4 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h7b50bb2_5 bioconda
perl-parent 0.243 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321hb9d3cd8_2 conda-forge
perl-scalar-list-utils 1.69 pl5321hb9d3cd8_0 conda-forge
perl-storable 3.15 pl5321hb9d3cd8_2 conda-forge
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
pip 25.1.1 pyh145f28c_0 conda-forge
pluggy 1.6.0 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
pytest 8.3.5 pyhd8ed1ab_0 conda-forge
python 3.13.3 hf636f53_101_cp313 conda-forge
python-dateutil 2.9.0.post0 pyhff2d567_1 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python_abi 3.13 7_cp313 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
readline 8.2 h8c095d6_2 conda-forge
requests 2.32.3 pyhd8ed1ab_1 conda-forge
rpsbproc 0.5.0 hd6d6fdc_3 bioconda
samtools 1.21 h96c455f_1 bioconda
seqtk 1.4 h577a1d6_3 bioconda
six 1.17.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_hd72426e_102 conda-forge
tomli 2.2.1 pyhd8ed1ab_1 conda-forge
typing_extensions 4.13.2 pyh29332c3_0 conda-forge
tzdata 2025b h78e105d_0 conda-forge
urllib3 2.4.0 pyhd8ed1ab_0 conda-forge
wget 1.21.4 hda4d442_0 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstandard 0.23.0 py313h536fd9c_2 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge
Basic information on how to use this tool:
- executable:
ectyper - help:
-h,--help - version:
--version - description: Prediction of Escherichia coli serotype, pathotype and shiga toxin tying from raw reads or assembled genome sequences.
This docker container contains a few databases used by ECTyper:
- O and H antigen database version 1.0 found in this JSON file
- species identification Mash sketch database created on 2023-10-03 and found here on Zenodo
- Toxin and pathotype signature marker sequences found in this JSON file
# run ECTyper on an assembled genome sequence using 2 threads. Also run QC verification steps and pathotype prediction.
ectyper -i E-coli-assembly.fasta -o ectyper-outdir -c 2 --verify --pathotype