Main tool :
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
_x86_64-microarch-level 3 2_x86_64_v3 conda-forge
alsa-lib 1.2.14 hb9d3cd8_0 conda-forge
aom 3.9.1 hac33072_0 conda-forge
at-spi2-atk 2.38.0 h0630a04_3 conda-forge
at-spi2-core 2.40.3 h0630a04_0 conda-forge
atk-1.0 2.38.0 h04ea711_2 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
biopython 1.85 py312h66e93f0_1 conda-forge
brotli 1.1.0 hb9d3cd8_3 conda-forge
brotli-bin 1.1.0 hb9d3cd8_3 conda-forge
brotli-python 1.1.0 py312h2ec8cdc_3 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.6.15 hbd8a1cb_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.18.4 h3394656_0 conda-forge
cairomm 1.16.2 ha770c72_1 conda-forge
cairomm-1.16 1.16.2 h7e731d7_1 conda-forge
certifi 2025.6.15 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py312h06ac9bb_0 conda-forge
charset-normalizer 3.4.2 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
contourpy 1.3.2 py312h68727a3_0 conda-forge
cuda-version 12.9 h4f385c5_3 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
dav1d 1.2.1 hd590300_0 conda-forge
dbus 1.16.2 h3c4dab8_0 conda-forge
dendropy 5.0.8 pyhdfd78af_1 bioconda
docopt 0.6.2 pyhd8ed1ab_2 conda-forge
epoxy 1.5.10 h166bdaf_1 conda-forge
expat 2.7.0 h5888daf_0 conda-forge
ffmpeg 7.1.1 gpl_h127656b_906 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_3 conda-forge
fontconfig 2.15.0 h7e30c49_1 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.58.4 py312h178313f_0 conda-forge
freetype 2.13.3 ha770c72_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gdk-pixbuf 2.42.12 hb9ae30d_0 conda-forge
gettext 0.24.1 h5888daf_0 conda-forge
gettext-tools 0.24.1 h5888daf_0 conda-forge
glib-tools 2.84.2 h4833e2c_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
graph-tool 2.97 py312h302780e_300 conda-forge
graph-tool-base 2.97 py312h55cd2aa_300 conda-forge
graphite2 1.3.14 h5888daf_0 conda-forge
gtk3 3.24.43 h0c6a113_5 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
h5py 3.14.0 nompi_py312h3faca00_100 conda-forge
harfbuzz 11.2.1 h3beb420_0 conda-forge
hdbscan 0.8.39 py312hc0a28a1_0 conda-forge
hdf5 1.14.6 nompi_h2d575fe_101 conda-forge
hicolor-icon-theme 0.17 ha770c72_2 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
joblib 1.5.1 pyhd8ed1ab_0 conda-forge
kernel-headers_linux-64 3.10.0 he073ed8_18 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.8 py312h84d6215_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.17 h717163a_0 conda-forge
ld_impl_linux-64 2.43 h1423503_5 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
level-zero 1.23.0 h84d6215_0 conda-forge
libabseil 20250127.1 cxx17_hbbce691_0 conda-forge
libaec 1.1.4 h3f801dc_0 conda-forge
libasprintf 0.24.1 h8e693c7_0 conda-forge
libasprintf-devel 0.24.1 h8e693c7_0 conda-forge
libass 0.17.3 h52826cd_2 conda-forge
libblas 3.9.0 32_h59b9bed_openblas conda-forge
libboost 1.86.0 h6c02f8c_3 conda-forge
libboost-python 1.86.0 py312hc39e661_3 conda-forge
libbrotlicommon 1.1.0 hb9d3cd8_3 conda-forge
libbrotlidec 1.1.0 hb9d3cd8_3 conda-forge
libbrotlienc 1.1.0 hb9d3cd8_3 conda-forge
libcap 2.75 h39aace5_0 conda-forge
libcblas 3.9.0 32_he106b2a_openblas conda-forge
libcups 2.3.3 hb8b1518_5 conda-forge
libcurl 8.14.1 h332b0f4_0 conda-forge
libdeflate 1.24 h86f0d12_0 conda-forge
libdrm 2.4.125 hb9d3cd8_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libegl 1.7.0 ha4b6fd6_2 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
libflac 1.4.3 h59595ed_0 conda-forge
libfreetype 2.13.3 ha770c72_1 conda-forge
libfreetype6 2.13.3 h48d6fc4_1 conda-forge
libgcc 15.1.0 h767d61c_3 conda-forge
libgcc-ng 15.1.0 h69a702a_3 conda-forge
libgcrypt-lib 1.11.1 hb9d3cd8_0 conda-forge
libgettextpo 0.24.1 h5888daf_0 conda-forge
libgettextpo-devel 0.24.1 h5888daf_0 conda-forge
libgfortran 15.1.0 h69a702a_3 conda-forge
libgfortran5 15.1.0 hcea5267_3 conda-forge
libgirepository 1.84.0 h0dcfedc_1 conda-forge
libgl 1.7.0 ha4b6fd6_2 conda-forge
libglib 2.84.2 h3618099_0 conda-forge
libglvnd 1.7.0 ha4b6fd6_2 conda-forge
libglx 1.7.0 ha4b6fd6_2 conda-forge
libgomp 15.1.0 h767d61c_3 conda-forge
libgpg-error 1.55 h3f2d84a_0 conda-forge
libhwloc 2.11.2 default_h0d58e46_1001 conda-forge
libiconv 1.18 h4ce23a2_1 conda-forge
libjpeg-turbo 3.1.0 hb9d3cd8_0 conda-forge
liblapack 3.9.0 32_h7ac8fdf_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libogg 1.3.5 hd0c01bc_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_0 conda-forge
libopenvino 2025.0.0 hdc3f47d_3 conda-forge
libopenvino-auto-batch-plugin 2025.0.0 h4d9b6c2_3 conda-forge
libopenvino-auto-plugin 2025.0.0 h4d9b6c2_3 conda-forge
libopenvino-hetero-plugin 2025.0.0 h981d57b_3 conda-forge
libopenvino-intel-cpu-plugin 2025.0.0 hdc3f47d_3 conda-forge
libopenvino-intel-gpu-plugin 2025.0.0 hdc3f47d_3 conda-forge
libopenvino-intel-npu-plugin 2025.0.0 hdc3f47d_3 conda-forge
libopenvino-ir-frontend 2025.0.0 h981d57b_3 conda-forge
libopenvino-onnx-frontend 2025.0.0 h0e684df_3 conda-forge
libopenvino-paddle-frontend 2025.0.0 h0e684df_3 conda-forge
libopenvino-pytorch-frontend 2025.0.0 h5888daf_3 conda-forge
libopenvino-tensorflow-frontend 2025.0.0 h684f15b_3 conda-forge
libopenvino-tensorflow-lite-frontend 2025.0.0 h5888daf_3 conda-forge
libopus 1.5.2 hd0c01bc_0 conda-forge
libpciaccess 0.18 hb9d3cd8_0 conda-forge
libpng 1.6.49 h943b412_0 conda-forge
libprotobuf 5.29.3 h501fc15_1 conda-forge
librsvg 2.58.4 he92a37e_3 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsqlite 3.50.2 h6cd9bfd_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.1.0 h8f9b012_3 conda-forge
libstdcxx-ng 15.1.0 h4852527_3 conda-forge
libsystemd0 257.7 h4e0b6ca_0 conda-forge
libtiff 4.7.0 hf01ce69_5 conda-forge
libudev1 257.7 hbe16f8c_0 conda-forge
libunwind 1.6.2 h9c3ff4c_0 conda-forge
liburing 2.10 h84d6215_0 conda-forge
libusb 1.0.29 h73b1eb8_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libva 2.22.0 h4f16b4b_2 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libvpx 1.14.1 hac33072_0 conda-forge
libwebp-base 1.5.0 h851e524_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.10.0 h65c71a3_0 conda-forge
libxml2 2.13.8 h4bc477f_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
lz4-c 1.10.0 h5888daf_1 conda-forge
mandrake 1.2.5 py312h85baa9b_0 conda-forge
matplotlib-base 3.10.3 py312hd3ec401_0 conda-forge
mpg123 1.32.9 hc50e24c_0 conda-forge
munkres 1.1.4 pyhd8ed1ab_1 conda-forge
narwhals 1.44.0 pyhe01879c_0 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.5 pyhe01879c_0 conda-forge
numpy 2.3.0 py312h6cf2f7f_0 conda-forge
ocl-icd 2.3.3 hb9d3cd8_0 conda-forge
openblas 0.3.30 pthreads_h6ec200e_0 conda-forge
opencl-headers 2025.06.13 h5888daf_0 conda-forge
openh264 2.6.0 hc22cd8d_0 conda-forge
openjpeg 2.5.3 h5fbd93e_0 conda-forge
openssl 3.5.0 h7b32b05_1 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.3.0 py312hf9745cd_0 conda-forge
pango 1.56.4 hadf4263_0 conda-forge
pcre2 10.45 hc749103_0 conda-forge
pillow 11.2.1 py312h80c1187_0 conda-forge
pip 25.1.1 pyh8b19718_0 conda-forge
pixman 0.46.2 h29eaf8c_0 conda-forge
plotly 6.2.0 pyhd8ed1ab_0 conda-forge
poppunk 2.7.6 py312hc15d307_0 bioconda
pp-sketchlib 2.1.5 py312hbf65ae3_1 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pugixml 1.15 h3f63f65_0 conda-forge
pulseaudio-client 17.0 hac146a9_1 conda-forge
pycairo 1.28.0 py312hac037c1_0 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pygobject 3.50.0 py312hf4b392c_1 conda-forge
pyparsing 3.2.3 pyhd8ed1ab_1 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.12.11 h9e4cc4f_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python_abi 3.12 7_cp312 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
qhull 2020.2 h434a139_5 conda-forge
rapidnj 2.3.2 h9948957_6 bioconda
readline 8.2 h8c095d6_2 conda-forge
requests 2.32.4 pyhd8ed1ab_0 conda-forge
scikit-learn 1.7.0 py312h7a48858_1 conda-forge
scipy 1.16.0 py312hf734454_0 conda-forge
sdl2 2.32.54 h3f2d84a_0 conda-forge
sdl3 3.2.16 he3e324a_0 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
sigcpp-3.0 3.6.0 h59595ed_0 conda-forge
six 1.17.0 pyhd8ed1ab_0 conda-forge
snappy 1.2.1 h8bd8927_1 conda-forge
sparsehash 2.0.4 hcb278e6_1 conda-forge
svt-av1 3.0.2 h5888daf_0 conda-forge
sysroot_linux-64 2.17 h0157908_18 conda-forge
tbb 2022.1.0 h4ce085d_0 conda-forge
threadpoolctl 3.6.0 pyhecae5ae_0 conda-forge
tk 8.6.13 noxft_hd72426e_102 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
treeswift 1.1.45 pyh7e72e81_0 bioconda
tzdata 2025b h78e105d_0 conda-forge
unicodedata2 16.0.0 py312h66e93f0_0 conda-forge
urllib3 2.5.0 pyhd8ed1ab_0 conda-forge
wayland 1.23.1 h3e06ad9_1 conda-forge
wayland-protocols 1.45 hd8ed1ab_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
x264 1!164.3095 h166bdaf_2 conda-forge
x265 3.5 h924138e_3 conda-forge
xkeyboard-config 2.45 hb9d3cd8_0 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.12 h4f16b4b_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxaw 1.0.16 hb9d3cd8_0 conda-forge
xorg-libxcomposite 0.4.6 hb9d3cd8_2 conda-forge
xorg-libxcursor 1.2.3 hb9d3cd8_0 conda-forge
xorg-libxdamage 1.1.6 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxfixes 6.0.1 hb9d3cd8_0 conda-forge
xorg-libxi 1.8.2 hb9d3cd8_0 conda-forge
xorg-libxinerama 1.1.5 h5888daf_1 conda-forge
xorg-libxmu 1.2.1 hb9d3cd8_1 conda-forge
xorg-libxpm 3.5.17 hb9d3cd8_1 conda-forge
xorg-libxrandr 1.5.4 hb9d3cd8_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxscrnsaver 1.2.4 hb9d3cd8_0 conda-forge
xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
xorg-libxtst 1.2.5 hb9d3cd8_3 conda-forge
xorg-xextproto 7.3.0 hb9d3cd8_1004 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstandard 0.23.0 py312h66e93f0_2 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge
Full documentation: https://poppunk.readthedocs.io/en/latest/
PopPUNK is also available as a webtool: https://www.poppunk.net/
PopPUNK is a tool for clustering genomes.
NOTE: This docker image is intended for the CLI usage of the PopPUNK tool. It has not been built with the full web-interface functionality in mind.
This example is for usage of PopPUNK for Streptococcus pneumoniae clustering using a database & reference files provided by the Global Pneumococcal Sequencing Project. An example S. pneumoniae genome can be obtained from here
# poppunk requires an input File Of File Names (FOFN). headerless TSV with a sample name (first column), followed by path to input FASTA
$ echo -e "SRR2912551\t/data/SRR2912551.fna.gz" > poppunk_input.tsv
# showing reference files, FASTA input, and poppunk_input.tsv
$ ls
GPS_v6/ GPS_v6_external_clusters.csv SRR2912551.fna.gz poppunk_input.tsv
# run the docker container interactively
# followed by poppunk command run inside the container
$ docker run --rm -ti -v ${PWD}:/data -u $(id -u):$(id -g) staphb/poppunk:2.6.2
$ poppunk_assign --db GPS_v6 --distances GPS_v6/GPS_v6.dists --query /data/poppunk_input.tsv --output docker_test --external-clustering GPS_v6_external_clusters.csv
PopPUNK: assign
(with backend: sketchlib v2.0.0
sketchlib: /opt/conda/envs/poppunk-env/lib/python3.10/site-packages/pp_sketchlib.cpython-310-x86_64-linux-gnu.so)
Graph-tools OpenMP parallelisation enabled: with 1 threads
Mode: Assigning clusters of query sequences
Loading previously refined model
Completed model loading
Sketching 1 genomes using 1 thread(s)
Progress (CPU): 1 / 1
Writing sketches to file
WARNING: versions of input databases sketches are different, results may not be compatible
Calculating distances using 1 thread(s)
Progress (CPU): 100.0%
Selected type isolate for distance QC is 10050_2#1
Network loaded: 42163 samples
Done