Main tool :
Additional tools installed via micromamba:
List of packages in environment: "/opt/conda/envs/poppunk-env"
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 3_x86_64_v3 conda-forge
alsa-lib 1.2.15.1 hb03c661_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 2.5.2 h39aace5_0 conda-forge
backports.zstd 1.3.0 py312h90b7ffd_0 conda-forge
biopython 1.86 py312h4c3975b_0 conda-forge
brotli 1.2.0 hed03a55_1 conda-forge
brotli-bin 1.2.0 hb03c661_1 conda-forge
brotli-python 1.2.0 py312hdb49522_1 conda-forge
bzip2 1.0.8 hda65f42_8 conda-forge
c-ares 1.34.6 hb03c661_0 conda-forge
ca-certificates 2025.11.12 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 he90730b_1 conda-forge
cairomm 1.16.2 ha770c72_1 conda-forge
cairomm-1.16 1.16.2 h7e731d7_1 conda-forge
certifi 2025.11.12 pyhd8ed1ab_0 conda-forge
cffi 2.0.0 py312h460c074_1 conda-forge
charset-normalizer 3.4.4 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
contourpy 1.3.3 py312hd9148b4_3 conda-forge
cuda-version 12.9 h4f385c5_3 conda-forge
cycler 0.12.1 pyhcf101f3_2 conda-forge
dav1d 1.2.1 hd590300_0 conda-forge
dbus 1.16.2 h24cb091_1 conda-forge
dendropy 5.0.8 pyhdfd78af_1 bioconda
docopt 0.6.2 pyhd8ed1ab_2 conda-forge
epoxy 1.5.10 hb03c661_2 conda-forge
expat 2.7.3 hecca717_0 conda-forge
ffmpeg 8.0.1 gpl_hf567e27_908 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 hc364b38_1 conda-forge
fonttools 4.61.1 py312h8a5da7c_0 conda-forge
freetype 2.14.1 ha770c72_0 conda-forge
fribidi 1.0.16 hb03c661_0 conda-forge
gdk-pixbuf 2.44.4 h2b0a6b4_0 conda-forge
gettext 0.25.1 h3f43e3d_1 conda-forge
gettext-tools 0.25.1 h3f43e3d_1 conda-forge
glib-tools 2.86.3 hf516916_0 conda-forge
glslang 16.1.0 hfd11570_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
graph-tool 2.98 py312h302780e_301 conda-forge
graph-tool-base 2.98 py312h8e10fa2_301 conda-forge
graphite2 1.3.14 hecca717_2 conda-forge
gtk3 3.24.43 h993cebd_6 conda-forge
h2 4.3.0 pyhcf101f3_0 conda-forge
h5py 3.15.1 nompi_py312ha4f8f14_101 conda-forge
harfbuzz 12.3.0 h6083320_0 conda-forge
hdbscan 0.8.41 py312h4f23490_0 conda-forge
hdf5 1.14.6 nompi_h1b119a7_104 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 78.1 h33c6efd_0 conda-forge
idna 3.11 pyhd8ed1ab_0 conda-forge
intel-gmmlib 22.9.0 hb700be7_0 conda-forge
intel-media-driver 25.3.4 hecca717_0 conda-forge
joblib 1.5.3 pyhd8ed1ab_0 conda-forge
kernel-headers_linux-64 5.14.0 he073ed8_3 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
kiwisolver 1.4.9 py312h0a2e395_2 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 2.45 default_hbd61a6d_105 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
level-zero 1.26.3 hb700be7_0 conda-forge
libabseil 20250512.1 cxx17_hba17884_0 conda-forge
libaec 1.1.4 h3f801dc_0 conda-forge
libasprintf 0.25.1 h3f43e3d_1 conda-forge
libasprintf-devel 0.25.1 h3f43e3d_1 conda-forge
libass 0.17.4 h96ad9f0_0 conda-forge
libblas 3.11.0 5_h4a7cf45_openblas conda-forge
libboost 1.86.0 hd24cca6_5 conda-forge
libboost-python 1.86.0 py312hf890105_5 conda-forge
libbrotlicommon 1.2.0 hb03c661_1 conda-forge
libbrotlidec 1.2.0 hb03c661_1 conda-forge
libbrotlienc 1.2.0 hb03c661_1 conda-forge
libcap 2.77 h3ff7636_0 conda-forge
libcblas 3.11.0 5_h0358290_openblas conda-forge
libcups 2.3.3 hb8b1518_5 conda-forge
libcurl 8.17.0 h4e3cde8_1 conda-forge
libdeflate 1.25 h17f619e_0 conda-forge
libdrm 2.4.125 hb03c661_1 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libegl 1.7.0 ha4b6fd6_2 conda-forge
libegl-devel 1.7.0 ha4b6fd6_2 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
libflac 1.5.0 he200343_1 conda-forge
libfreetype 2.14.1 ha770c72_0 conda-forge
libfreetype6 2.14.1 h73754d4_0 conda-forge
libgcc 15.2.0 he0feb66_16 conda-forge
libgcc-ng 15.2.0 h69a702a_16 conda-forge
libgettextpo 0.25.1 h3f43e3d_1 conda-forge
libgettextpo-devel 0.25.1 h3f43e3d_1 conda-forge
libgfortran 15.2.0 h69a702a_16 conda-forge
libgfortran5 15.2.0 h68bc16d_16 conda-forge
libgirepository 1.84.0 hac26d07_4 conda-forge
libgl 1.7.0 ha4b6fd6_2 conda-forge
libgl-devel 1.7.0 ha4b6fd6_2 conda-forge
libglib 2.86.3 h6548e54_0 conda-forge
libglvnd 1.7.0 ha4b6fd6_2 conda-forge
libglx 1.7.0 ha4b6fd6_2 conda-forge
libglx-devel 1.7.0 ha4b6fd6_2 conda-forge
libgomp 15.2.0 he0feb66_16 conda-forge
libhwloc 2.12.1 default_hafda6a7_1003 conda-forge
libiconv 1.18 h3b78370_2 conda-forge
libjpeg-turbo 3.1.2 hb03c661_0 conda-forge
liblapack 3.11.0 5_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
libogg 1.3.5 hd0c01bc_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_4 conda-forge
libopenvino 2025.4.1 hb56ce9e_0 conda-forge
libopenvino-auto-batch-plugin 2025.4.1 hd85de46_0 conda-forge
libopenvino-auto-plugin 2025.4.1 hd85de46_0 conda-forge
libopenvino-hetero-plugin 2025.4.1 hd41364c_0 conda-forge
libopenvino-intel-cpu-plugin 2025.4.1 hb56ce9e_0 conda-forge
libopenvino-intel-gpu-plugin 2025.4.1 hb56ce9e_0 conda-forge
libopenvino-intel-npu-plugin 2025.4.1 hb56ce9e_0 conda-forge
libopenvino-ir-frontend 2025.4.1 hd41364c_0 conda-forge
libopenvino-onnx-frontend 2025.4.1 h1862bb8_0 conda-forge
libopenvino-paddle-frontend 2025.4.1 h1862bb8_0 conda-forge
libopenvino-pytorch-frontend 2025.4.1 hecca717_0 conda-forge
libopenvino-tensorflow-frontend 2025.4.1 h0767aad_0 conda-forge
libopenvino-tensorflow-lite-frontend 2025.4.1 hecca717_0 conda-forge
libopus 1.6 h0fd0de7_0 conda-forge
libpciaccess 0.18 hb9d3cd8_0 conda-forge
libpng 1.6.53 h421ea60_0 conda-forge
libprotobuf 6.31.1 h49aed37_4 conda-forge
librsvg 2.60.0 h61e6d4b_0 conda-forge
libsndfile 1.2.2 hc7d488a_2 conda-forge
libsqlite 3.51.1 hf4e2dac_1 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.2.0 h934c35e_16 conda-forge
libstdcxx-ng 15.2.0 hdf11a46_16 conda-forge
libsystemd0 258.3 h6569c3e_0 conda-forge
libtiff 4.7.1 h9d88235_1 conda-forge
libudev1 258.3 h6569c3e_0 conda-forge
libunwind 1.8.3 h65a8314_0 conda-forge
liburing 2.12 hb700be7_0 conda-forge
libusb 1.0.29 h73b1eb8_0 conda-forge
libuuid 2.41.3 h5347b49_0 conda-forge
libva 2.23.0 he1eb515_0 conda-forge
libvorbis 1.3.7 h54a6638_2 conda-forge
libvpl 2.15.0 h54a6638_1 conda-forge
libvpx 1.15.2 hecca717_0 conda-forge
libvulkan-loader 1.4.328.1 h5279c79_0 conda-forge
libwebp-base 1.6.0 hd42ef1d_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.13.1 hca5e8e5_0 conda-forge
libxml2 2.15.1 he237659_1 conda-forge
libxml2-16 2.15.1 hca6bf5a_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
mandrake 1.2.5 py312h85baa9b_0 conda-forge
matplotlib-base 3.10.8 py312he3d6523_0 conda-forge
mpg123 1.32.9 hc50e24c_0 conda-forge
munkres 1.1.4 pyhd8ed1ab_1 conda-forge
narwhals 2.14.0 pyhcf101f3_0 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.6.1 pyhcf101f3_0 conda-forge
numpy 2.4.0 py312h33ff503_0 conda-forge
ocl-icd 2.3.3 hb9d3cd8_0 conda-forge
openblas 0.3.30 pthreads_h6ec200e_4 conda-forge
opencl-headers 2025.06.13 h5888daf_0 conda-forge
openh264 2.6.0 hc22cd8d_0 conda-forge
openjpeg 2.5.4 h55fea9a_0 conda-forge
openssl 3.6.0 h26f9b46_0 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.3.3 py312hf79963d_1 conda-forge
pango 1.56.4 hadf4263_0 conda-forge
pcre2 10.47 haa7fec5_0 conda-forge
pillow 12.0.0 py312h50c33e8_2 conda-forge
pip 25.3 pyh8b19718_0 conda-forge
pixman 0.46.4 h54a6638_1 conda-forge
plotly 6.5.0 pyhd8ed1ab_0 conda-forge
poppunk 2.7.7 py312hc15d307_0 bioconda
pp-sketchlib 2.1.5 py312ha1e97ca_3 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pugixml 1.15 h3f63f65_0 conda-forge
pulseaudio-client 17.0 h9a6aba3_3 conda-forge
pycairo 1.29.0 py312h2596900_0 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pygobject 3.54.5 py312hd86a0b5_2 conda-forge
pyparsing 3.3.1 pyhcf101f3_0 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.12.12 hd63d673_1_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-tzdata 2025.3 pyhd8ed1ab_0 conda-forge
python_abi 3.12 8_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 8.3 h853b02a_0 conda-forge
requests 2.32.5 pyhcf101f3_1 conda-forge
scikit-learn 1.8.0 np2py312h3226591_1 conda-forge
scipy 1.16.3 py312h54fa4ab_2 conda-forge
sdl2 2.32.56 h54a6638_0 conda-forge
sdl3 3.2.28 h3b84278_0 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
shaderc 2025.5 h3e344bc_0 conda-forge
sigcpp-3.0 3.6.0 h59595ed_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
snappy 1.2.2 h03e3b7b_1 conda-forge
sparsehash 2.0.4 hcb278e6_1 conda-forge
spirv-tools 2025.4 hb700be7_0 conda-forge
svt-av1 3.1.2 hecca717_0 conda-forge
sysroot_linux-64 2.34 h087de78_3 conda-forge
tbb 2022.3.0 h8d10470_1 conda-forge
threadpoolctl 3.6.0 pyhecae5ae_0 conda-forge
tk 8.6.13 noxft_ha0e22de_103 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
treeswift 1.1.45 pyh7e72e81_0 bioconda
tzdata 2025c hc9c84f9_1 conda-forge
unicodedata2 17.0.0 py312h4c3975b_1 conda-forge
urllib3 2.6.2 pyhd8ed1ab_0 conda-forge
wayland 1.24.0 hd6090a7_1 conda-forge
wayland-protocols 1.47 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 2.46 hb03c661_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 hb03c661_1 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 hb03c661_1 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxfixes 6.0.2 hb03c661_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-libxxf86vm 1.1.6 hb9d3cd8_0 conda-forge
xorg-xextproto 7.3.0 hb9d3cd8_1004 conda-forge
xorg-xorgproto 2025.1 hb03c661_0 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zlib-ng 2.3.2 hceb46e0_1 conda-forge
zstandard 0.25.0 py312h5253ce2_1 conda-forge
zstd 1.5.7 hb78ec9c_6 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