Main tool : piranha
Additional tools installed via micromamba:
List of packages in environment: "/opt/conda/envs/piranha"
Name Version Build Channel
──────────────────────────────────────────────────────────────────────────────────────────────────
Mako 1.2.0 pypi_0 pypi
_openmp_mutex 5.1 52_gnu pkgs/main
alsa-lib 1.2.16.1 hb03c661_0 conda-forge
appdirs 1.4.4 pyhd8ed1ab_1 conda-forge
argparse-dataclass 2.0.0 pyhd8ed1ab_1 conda-forge
attrs 26.1.0 pyhcf101f3_0 conda-forge
aws-c-auth 0.10.1 ha62d5e7_3 conda-forge
aws-c-cal 0.9.13 h2c9d079_1 conda-forge
aws-c-common 0.12.6 hb03c661_0 conda-forge
aws-c-compression 0.3.2 h8b1a151_0 conda-forge
aws-c-http 0.10.13 h4bacb7b_0 conda-forge
aws-c-io 0.26.3 hb18f61d_2 conda-forge
aws-c-s3 0.12.0 h1b28b03_1 pkgs/main
aws-c-sdkutils 0.2.4 h8b1a151_4 conda-forge
aws-checksums 0.2.10 h8b1a151_0 conda-forge
backports.zstd 1.6.0 py312h90b7ffd_0 conda-forge
tabix 1.11 hdfd78af_0 bioconda
tabixpp 1.1.2 hbefcdb2_4 bioconda
tabulate 0.10.0 pyhcf101f3_0 conda-forge
tar 1.35 h3b78370_0 conda-forge
tenacity 9.1.4 pyhcf101f3_0 conda-forge
tensordict 0.1.2 pyh6074d0b_0 conda-forge
throttler 1.2.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h366c992_103 conda-forge
toml 0.10.2 pyhcf101f3_3 conda-forge
tqdm 4.68.3 pyh8f84b5b_0 conda-forge
traitlets 5.15.1 pyhcf101f3_0 conda-forge
typing-extensions 4.15.0 h396c80c_0 conda-forge
typing_extensions 4.15.0 pyhcf101f3_0 conda-forge
tzdata 2025c hc9c84f9_1 conda-forge
urllib3 2.7.0 pyhd8ed1ab_0 conda-forge
vcflib 1.0.15 h3fa9d83_1 bioconda
wget 1.25.0 h653f8fd_1 conda-forge
wheel 0.47.0 pyhd8ed1ab_0 conda-forge
wrapt 1.17.0 py312h5eee18b_0 pkgs/main
wurlitzer 3.1.1 pyhd8ed1ab_1 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.13 he1eb515_0 conda-forge
xorg-libxau 1.0.12 hb03c661_1 conda-forge
xorg-libxdmcp 1.1.5 hb03c661_1 conda-forge
xorg-libxext 1.3.7 hb03c661_0 conda-forge
xorg-libxfixes 6.0.2 hb03c661_0 conda-forge
xorg-libxi 1.8.3 hb03c661_0 conda-forge
xorg-libxrandr 1.5.5 hb03c661_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
yaml 0.2.5 h280c20c_3 conda-forge
yte 1.9.4 pyhd8ed1ab_0 conda-forge
zlib 1.3.2 h25fd6f3_2 conda-forge
zstd 1.5.7 hb78ec9c_6 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