Main tool : piranha
Additional tools installed via micromamba:
List of packages in environment: "/opt/conda/envs/piranha"
Name Version Build Channel
─────────────────────────────────────────────────────────────────────────────────
Keras-Preprocessing 1.1.2 pypi_0 pypi
Mako 1.2.0 pypi_0 pypi
Markdown 3.8.2 pypi_0 pypi
Werkzeug 3.1.3 pypi_0 pypi
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
absl-py 2.3.0 pypi_0 pypi
alsa-lib 1.2.11 hd590300_1 conda-forge
amply 0.1.6 pyhd8ed1ab_1 conda-forge
appdirs 1.4.4 pyhd8ed1ab_1 conda-forge
astunparse 1.6.3 pypi_0 pypi
attrs 25.3.0 pyh71513ae_0 conda-forge
bcftools 1.20 h8b25389_1 bioconda
biopython 1.85 pypi_0 pypi
brotli-python 1.1.0 py310hf71b8c6_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
cachetools 5.5.2 pypi_0 pypi
cairo 1.16.0 he5ede1b_6 pkgs/main
certifi 2025.6.15 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py310h8deb56e_0 conda-forge
charset-normalizer 3.4.2 pyhd8ed1ab_0 conda-forge
coin-or-cbc 2.10.12 h8b142ea_1 conda-forge
coin-or-cgl 0.60.7 h516709c_0 conda-forge
coin-or-clp 1.17.8 h1ee7a9c_0 conda-forge
coin-or-osi 0.108.10 haf5fa05_0 conda-forge
coin-or-utils 2.11.11 hee58242_0 conda-forge
coincbc 2.10.12 2_metapackage conda-forge
configargparse 1.7.1 pyhe01879c_0 conda-forge
connection_pool 0.0.3 pyhd3deb0d_0 conda-forge
contourpy 1.3.2 pypi_0 pypi
coreutils 9.1 h166bdaf_0 conda-forge
cycler 0.12.1 pypi_0 pypi
datrie 0.8.2 py310ha75aee5_8 conda-forge
docutils 0.21.2 pyhd8ed1ab_1 conda-forge
dpath 2.2.0 pyha770c72_0 conda-forge
edlib 1.3.9.post1 pypi_0 pypi
eigen 3.4.0 h00ab1b0_0 conda-forge
expat 2.7.0 h5888daf_0 conda-forge
flatbuffers 25.2.10 pypi_0 pypi
flopp 0.2.0 h4ac6f70_0 bioconda
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 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.58.4 pypi_0 pypi
freebayes 1.3.6 hb0f3ef8_7 bioconda
freetype 2.12.1 h267a509_2 conda-forge
gast 0.4.0 pypi_0 pypi
gawk 5.3.1 hcd3d067_0 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
gitdb 4.0.12 pyhd8ed1ab_0 conda-forge
gitpython 3.1.44 pyhff2d567_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
google-auth 2.40.3 pypi_0 pypi
google-auth-oauthlib 0.4.6 pypi_0 pypi
google-pasta 0.2.0 pypi_0 pypi
graphite2 1.3.14 h5888daf_0 conda-forge
grpcio 1.73.1 pypi_0 pypi
gsl 2.7 he838d99_0 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
h5py 3.10.0 pypi_0 pypi
harfbuzz 10.2.0 hf296adc_0 pkgs/main
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
htslib 1.21 h5efdd21_0 bioconda
humanfriendly 10.0 pyh707e725_8 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
importlib_resources 6.5.2 pyhd8ed1ab_0 conda-forge
intervaltree 3.1.0 pypi_0 pypi
iqtree 2.4.0 h503566f_0 bioconda
jclusterfunk 0.0.25 1 cov-ert
jinja2 3.1.6 pyhd8ed1ab_0 conda-forge
jsoncpp 1.9.6 hf42df4d_1 conda-forge
jsonschema 4.24.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2025.4.1 pyh29332c3_0 conda-forge
jupyter_core 5.8.1 pyh31011fe_0 conda-forge
k8 0.2.5 hdcf5f25_4 bioconda
keras 2.10.0 pypi_0 pypi
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.8 pypi_0 pypi
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.43 h1423503_5 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
libasprintf 0.24.1 h8e693c7_0 conda-forge
libblas 3.9.0 32_h59b9bed_openblas conda-forge
libcblas 3.9.0 32_he106b2a_openblas conda-forge
libclang 18.1.1 pypi_0 pypi
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.8.0 hca28451_1 conda-forge
libdeflate 1.20 hd590300_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_3 conda-forge
libgcc-ng 15.1.0 h69a702a_3 conda-forge
libgettextpo 0.24.1 h5888daf_0 conda-forge
libgfortran 15.1.0 h69a702a_3 conda-forge
libgfortran-ng 15.1.0 h69a702a_3 conda-forge
libgfortran5 15.1.0 hcea5267_3 conda-forge
libglib 2.80.2 hf974151_0 conda-forge
libgomp 15.1.0 h767d61c_3 conda-forge
libiconv 1.18 h4ce23a2_1 conda-forge
libidn2 2.3.8 ha4ef2c3_0 conda-forge
libjpeg-turbo 3.1.0 hb9d3cd8_0 conda-forge
liblapack 3.9.0 32_h7ac8fdf_openblas conda-forge
liblapacke 3.9.0 32_he2f377e_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
liblzma-devel 5.8.1 hb9d3cd8_2 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_0 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx 15.1.0 h8f9b012_3 conda-forge
libstdcxx-ng 15.1.0 h4852527_3 conda-forge
libtiff 4.6.0 h1dd3fc0_3 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_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
libzlib 1.2.13 h4ab18f5_6 conda-forge
mafft 7.526 h4bc722e_0 conda-forge
mappy 2.30 pypi_0 pypi
markupsafe 3.0.2 py310h89163eb_1 conda-forge
matplotlib 3.10.3 pypi_0 pypi
medaka 1.12.1 pypi_0 pypi
minimap2 2.17 h5bf99c6_4 bioconda
mpfr 4.2.1 h90cbb55_3 conda-forge
nbformat 5.10.4 pyhd8ed1ab_1 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
numpy 1.26.4 pypi_0 pypi
oauthlib 3.3.1 pypi_0 pypi
ont-fast5-api 4.1.3 pypi_0 pypi
ont-parasail 1.3.4 pypi_0 pypi
openjdk 22.0.1 hb622114_0 conda-forge
openssl 3.5.0 h7b32b05_1 conda-forge
opt_einsum 3.4.0 pypi_0 pypi
packaging 25.0 pyh29332c3_1 conda-forge
pandas 1.5.3 pypi_0 pypi
parallel 20250622 ha770c72_0 conda-forge
pcre2 10.43 hcad00b1_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pillow 11.2.1 pypi_0 pypi
pip 25.1.1 pyh8b19718_0 conda-forge
piranha 1.5.3 pypi_0 pypi
pixman 0.46.2 h29eaf8c_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_2 conda-forge
plac 1.4.5 pyhd8ed1ab_0 conda-forge
platformdirs 4.3.8 pyhe01879c_0 conda-forge
progressbar33 2.4 pypi_0 pypi
protobuf 3.19.6 pypi_0 pypi
psutil 7.0.0 py310ha75aee5_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pulp 2.7.0 py310hff52083_1 conda-forge
pyabpoa 1.5.4 pypi_0 pypi
pyasn1 0.6.1 pypi_0 pypi
pyasn1_modules 0.4.2 pypi_0 pypi
pycparser 2.22 pyh29332c3_1 conda-forge
pyparsing 3.2.3 pyhd8ed1ab_1 conda-forge
pysam 0.23.3 pypi_0 pypi
pysocks 1.7.1 pyha55dd90_7 conda-forge
pyspoa 0.2.1 pypi_0 pypi
python 3.10.14 hd12c33a_0_cpython conda-forge
python-dateutil 2.9.0.post0 pypi_0 pypi
python-fastjsonschema 2.21.1 pyhd8ed1ab_0 conda-forge
python_abi 3.10 7_cp310 conda-forge
pytz 2025.2 pypi_0 pypi
pyyaml 6.0.2 py310h89163eb_2 conda-forge
rasusa 0.7.1 h031d066_2 bioconda
readline 8.2 h8c095d6_2 conda-forge
referencing 0.36.2 pyh29332c3_0 conda-forge
requests 2.32.4 pyhd8ed1ab_0 conda-forge
requests-oauthlib 2.0.0 pypi_0 pypi
reretry 0.11.8 pyhd8ed1ab_1 conda-forge
rpds-py 0.25.1 py310hbcd0ec0_0 conda-forge
rsa 4.9.1 pypi_0 pypi
samtools 1.20 h50ea8bc_1 bioconda
scipy 1.15.3 pypi_0 pypi
setuptools 80.9.0 pyhff2d567_0 conda-forge
six 1.17.0 pypi_0 pypi
smart_open 7.1.0 pyhd8ed1ab_0 conda-forge
smmap 5.0.2 pyhd8ed1ab_0 conda-forge
snakemake-minimal 7.32.4 pyhdfd78af_1 bioconda
snipit 1.6 pypi_0 pypi
sortedcontainers 2.4.0 pypi_0 pypi
stopit 1.1.2 pyhd8ed1ab_1 conda-forge
tabix 1.11 hdfd78af_0 bioconda
tabixpp 1.1.2 h27d5293_3 bioconda
tabulate 0.9.0 pyhd8ed1ab_2 conda-forge
tensorboard 2.10.1 pypi_0 pypi
tensorboard-data-server 0.6.1 pypi_0 pypi
tensorboard-plugin-wit 1.8.1 pypi_0 pypi
tensorflow 2.10.1 pypi_0 pypi
tensorflow-estimator 2.10.0 pypi_0 pypi
tensorflow-io-gcs-filesystem 0.37.1 pypi_0 pypi
termcolor 3.1.0 pypi_0 pypi
throttler 1.2.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toposort 1.10 pyhd8ed1ab_1 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
typing_extensions 4.14.0 pyhe01879c_0 conda-forge
tzdata 2025b h78e105d_0 conda-forge
urllib3 2.5.0 pyhd8ed1ab_0 conda-forge
vcflib 1.0.10 hdcf5f25_1 bioconda
wfa2-lib 2.3.5 h9948957_3 bioconda
wget 1.21.4 hda4d442_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
wrapt 1.17.2 py310ha75aee5_0 conda-forge
wurlitzer 3.1.1 pypi_0 pypi
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-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-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
xorg-libxtst 1.2.5 hb9d3cd8_3 conda-forge
xz 5.8.1 hbcc6ac9_2 conda-forge
xz-gpl-tools 5.8.1 hbcc6ac9_2 conda-forge
xz-tools 5.8.1 hb9d3cd8_2 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yte 1.8.1 pyha770c72_0 conda-forge
zipp 3.23.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h4ab18f5_6 conda-forge
zstandard 0.23.0 py310ha75aee5_2 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
Full documentation: https://github.com/polio-nanopore/piranha
Poliovirus Investigation Resource Automating Nanopore Haplotype Analysis.
piranha is a tool in development as part of the Poliovirus Sequencing Consortium. It runs an automated analysis pipeline for sequencing VP1 regions of the poliovirus or non-polio enterovirus genome (whole genome analysis to be implemented soon) and produces an interactive report alongside the consensus data.
# run Piranha on a directory of FASTQs (Guppy output)
piranha -i /piranha/test/pak_run/demultiplexed --verbose -b piranha/test/pak_run/barcodes01.csv -t 2 2>&1 | tee piranha.log