Main tool : Kleborate
Additional tools:
- amrfinderplus 4.0.23 with database version 2025-07-16.1
- bcftools 1.22
- biopython 1.85
- dna-features-viewer 3.1.5
- ectyper 2.0.0
- ezclermont 0.7.0
- hmmer 3.4
- htslib 1.22
- mash 2.3
- matplotlib 3.9.4
- minimap2 2.30
- numpy 2.0.2
- python 3.9.23
- kaptive 3.1.0
- stxtyper 1.0.42
- samtools 1.22.1
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 1.22 h3a4d415_1 bioconda
biopython 1.85 py39h8cd3c5a_1 conda-forge
blast 2.17.0 h66d330f_0 bioconda
bowtie2 2.5.4 he96a11b_6 bioconda
brotli-python 1.1.0 py39hf88036b_3 conda-forge
bzip2 1.0.8 hda65f42_8 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.11.12 hbd8a1cb_0 conda-forge
capnproto 1.0.2 h766bdaa_3 conda-forge
certifi 2025.8.3 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py39h15c3d72_0 conda-forge
charset-normalizer 3.4.3 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
contourpy 1.3.0 pypi_0 pypi
coverage 7.10.4 py39heb7d2ae_0 conda-forge
curl 8.17.0 h4e3cde8_0 conda-forge
cycler 0.12.1 pypi_0 pypi
dna_features_viewer 3.1.5 pypi_0 pypi
ectyper 2.0.0 pyhdfd78af_4 bioconda
entrez-direct 24.0 he881be0_0 bioconda
exceptiongroup 1.3.0 pyhd8ed1ab_0 conda-forge
ezclermont 0.7.0 pyhdfd78af_0 bioconda
fonttools 4.60.1 pypi_0 pypi
gsl 2.7 he838d99_0 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
hmmer 3.4 hb6cb901_4 bioconda
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
htslib 1.22.1 h566b1c6_0 bioconda
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
importlib_resources 6.5.2 pypi_0 pypi
iniconfig 2.0.0 pyhd8ed1ab_1 conda-forge
k8 1.2 he8db53b_6 bioconda
kaptive 3.1.0 pypi_0 pypi
kernel-headers_linux-64 5.14.0 he073ed8_2 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
kiwisolver 1.4.7 pypi_0 pypi
kleborate 3.2.4 pypi_0 pypi
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.45 h1aa0949_0 conda-forge
libblas 3.11.0 1_h4a7cf45_openblas conda-forge
libcblas 3.11.0 1_h0358290_openblas conda-forge
libcurl 8.17.0 h4e3cde8_0 conda-forge
libdeflate 1.25 h17f619e_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.3 hecca717_0 conda-forge
libffi 3.5.2 h9ec8514_0 conda-forge
libgcc 15.2.0 h767d61c_7 conda-forge
libgcc-ng 15.2.0 h69a702a_7 conda-forge
libgfortran 15.2.0 h69a702a_7 conda-forge
libgfortran-ng 15.2.0 h69a702a_7 conda-forge
libgfortran5 15.2.0 hcd61629_7 conda-forge
libgomp 15.2.0 h767d61c_7 conda-forge
libidn2 2.3.8 hfac485b_1 conda-forge
liblapack 3.11.0 1_h47877c9_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
libnghttp2 1.67.0 had1ee68_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_4 conda-forge
libsqlite 3.51.0 hee844dc_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.2.0 h8f9b012_7 conda-forge
libstdcxx-ng 15.2.0 h4852527_7 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.41.2 he9a06e4_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
matplotlib 3.9.4 pypi_0 pypi
minimap2 2.30 h577a1d6_0 bioconda
mpi 1.0 openmpi conda-forge
ncbi-amrfinderplus 4.0.23 hf69ffd2_0 bioconda
ncbi-vdb 3.2.1 h9948957_0 bioconda
ncurses 6.5 h2d0b736_3 conda-forge
numpy 2.0.2 py39h9cb892a_1 conda-forge
openmpi 4.1.6 hc5af2df_101 conda-forge
openssl 3.6.0 h26f9b46_0 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.3.1 py39h1b6b32d_0 conda-forge
pcre2 10.45 hc749103_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
perl-archive-tar 3.04 pl5321hdfd78af_0 bioconda
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-common-sense 3.75 pl5321hd8ed1ab_0 conda-forge
perl-compress-raw-bzip2 2.214 pl5321hda65f42_0 conda-forge
perl-compress-raw-zlib 2.214 pl5321h4dac143_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 2.213 pl5321h503566f_0 bioconda
perl-io-zlib 1.15 pl5321hdfd78af_1 bioconda
perl-json 4.10 pl5321hdfd78af_1 bioconda
perl-json-xs 4.04 pl5321h9948957_0 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 1.70 pl5321hb03c661_0 conda-forge
perl-storable 3.15 pl5321hb9d3cd8_2 conda-forge
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
pillow 11.3.0 pypi_0 pypi
pip 25.2 pyh8b19718_0 conda-forge
pluggy 1.6.0 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pygments 2.19.2 pyhd8ed1ab_0 conda-forge
pyparsing 3.2.5 pypi_0 pypi
pysocks 1.7.1 pyha55dd90_7 conda-forge
pytest 8.4.1 pyhd8ed1ab_0 conda-forge
python 3.9.23 hc30ae73_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python_abi 3.9 8_cp39 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
readline 8.2 h8c095d6_2 conda-forge
requests 2.32.5 pyhd8ed1ab_0 conda-forge
samtools 1.22.1 h96c455f_0 bioconda
seqtk 1.5 h577a1d6_1 bioconda
setuptools 80.9.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
sysroot_linux-64 2.34 h087de78_2 conda-forge
tk 8.6.13 noxft_ha0e22de_103 conda-forge
tomli 2.2.1 pyhe01879c_2 conda-forge
typing_extensions 4.14.1 pyhe01879c_0 conda-forge
tzdata 2025b h78e105d_0 conda-forge
urllib3 2.5.0 pyhd8ed1ab_0 conda-forge
wget 1.25.0 hc2d8bac_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
zipp 3.23.0 pypi_0 pypi
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstandard 0.23.0 py39hd399759_3 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge
Full documentation: https://kleborate.readthedocs.io/en/latest/index.html
Description:
Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:
- MLST sequence type
- species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.)
- ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)
- virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)
- antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases
- K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive
Kleborate has modules for both Klebsiella and Escherichia species. The available presets and modules are listed below.
Available presets: kpsc, kosc, escherichia
Available modules for Kleborate
-------------------------------
enterobacterales__species: Mash-based species detection for enterobacterales species
escherichia__mlst_achtman: chromosomal MLST for Escherichia coli using the Achtman scheme
escherichia__mlst_pasteur: chromosomal MLST for Escherichia coli using the Pasteur scheme
general__contig_stats: basic stats on the assembly's contigs
klebsiella__abst: MLST on the KpSC aerobactin locus (iuc genes)
klebsiella__cbst: MLST on the KpSC colibactin locus (clb genes)
klebsiella__rmpa2: typing for the rmpA2 gene
klebsiella__rmst: MLST on the KpSC Rmp locus (rmp genes)
klebsiella__smst: MLST on the KpSC salmochelin locus (iro genes)
klebsiella__ybst: MLST on the KpSC yersiniabactin locus (ybt and irp genes)
klebsiella_oxytoca_complex__mlst: chromosomal MLST for the Klebsiella oxytoca species complex
klebsiella_pneumo_complex__amr: Genotyping acquired genes and mutations for the Klebsiella pneumoniae species complex
klebsiella_pneumo_complex__kaptive: In silico serotyping of K and L locus for the Klebsiella pneumoniae species complex
klebsiella_pneumo_complex__mlst: chromosomal MLST for the Klebsiella pneumoniae species complex
klebsiella_pneumo_complex__resistance_class_count: Resistance gene classes count, excluding the Bla_chr class which is intrinsicresults of the
klebsiella_pneumo_complex__amr module
klebsiella_pneumo_complex__resistance_gene_count: Resistance genes counts, excluding the Bla class which is intrinsicresults of the
klebsiella_pneumo_complex__amr module
klebsiella_pneumo_complex__resistance_score: resistance score (0-3) for the Klebsiella pneumoniae species complex, based on the results of the
klebsiella_pneumo_complex__amr module
klebsiella_pneumo_complex__virulence_score: virulence score (0-5) for the Klebsiella pneumoniae species complex, based on the results of the abst, cbst
and ybst modules
klebsiella_pneumo_complex__wzi: WZI typing for K antigen prediction
kleborate -a sample.fasta -o outdir -p preset