Main tool : Panaroo
Additional tools installed via micromamba:
Name Version Build Channel
───────────────────────────────────────────────────────────────────────────────
_openmp_mutex 4.5 3_kmp_llvm conda-forge
alsa-lib 1.2.14 hb9d3cd8_0 conda-forge
aragorn 1.2.41 h7b50bb2_5 bioconda
argcomplete 3.6.2 pyhd8ed1ab_0 conda-forge
argh 0.31.3 pyhd8ed1ab_1 conda-forge
arpack 3.9.1 nompi_hf03ea27_102 conda-forge
barrnap 0.9 hdfd78af_4 bioconda
bedtools 2.31.1 h13024bc_3 bioconda
biocode 0.12.0 pyhdfd78af_0 bioconda
biopython 1.85 py39h8cd3c5a_1 conda-forge
blast 2.16.0 h66d330f_5 bioconda
brotli 1.1.0 hb9d3cd8_2 conda-forge
brotli-bin 1.1.0 hb9d3cd8_2 conda-forge
brotli-python 1.1.0 py39hf88036b_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.4.26 hbd8a1cb_0 conda-forge
cairo 1.18.4 h3394656_0 conda-forge
capnproto 1.0.2 h766bdaa_3 conda-forge
cd-hit 4.8.1 h5ca1c30_13 bioconda
certifi 2025.4.26 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py39h15c3d72_0 conda-forge
charset-normalizer 3.4.2 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
contourpy 1.3.0 py39h74842e3_2 conda-forge
curl 8.13.0 h332b0f4_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
dendropy 5.0.6 pyhdfd78af_0 bioconda
entrez-direct 22.4 he881be0_0 bioconda
expat 2.7.0 h5888daf_0 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 4.57.0 py39h9399b63_0 conda-forge
freetype 2.13.3 ha770c72_1 conda-forge
gawk 5.3.1 hcd3d067_0 conda-forge
gffutils 0.13 pyh7cba7a3_0 bioconda
giflib 5.2.2 hd590300_0 conda-forge
glpk 5.0 h445213a_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
gsl 2.7 he838d99_0 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
harfbuzz 11.1.0 h3beb420_0 conda-forge
hmmer 3.4 hb6cb901_4 bioconda
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
importlib-metadata 8.6.1 pyha770c72_0 conda-forge
importlib-resources 6.5.2 pyhd8ed1ab_0 conda-forge
importlib_resources 6.5.2 pyhd8ed1ab_0 conda-forge
infernal 1.1.4 h779adbc_0 bioconda
intbitset 3.0.2 py39hd1e30aa_1 conda-forge
jinja2 3.1.6 pyhd8ed1ab_0 conda-forge
joblib 1.5.0 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.7 py39h74842e3_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.17 h717163a_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
libasprintf 0.24.1 h8e693c7_0 conda-forge
libblas 3.9.0 31_h59b9bed_openblas conda-forge
libbrotlicommon 1.1.0 hb9d3cd8_2 conda-forge
libbrotlidec 1.1.0 hb9d3cd8_2 conda-forge
libbrotlienc 1.1.0 hb9d3cd8_2 conda-forge
libcblas 3.9.0 31_he106b2a_openblas conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.13.0 h332b0f4_0 conda-forge
libdeflate 1.23 h86f0d12_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
libfreetype 2.13.3 ha770c72_1 conda-forge
libfreetype6 2.13.3 h48d6fc4_1 conda-forge
libgcc 14.2.0 h767d61c_2 conda-forge
libgcc-ng 14.2.0 h69a702a_2 conda-forge
libgettextpo 0.24.1 h5888daf_0 conda-forge
libgfortran 14.2.0 h69a702a_2 conda-forge
libgfortran-ng 14.2.0 h69a702a_2 conda-forge
libgfortran5 14.2.0 hf1ad2bd_2 conda-forge
libglib 2.84.1 h3618099_1 conda-forge
libgomp 14.2.0 h767d61c_2 conda-forge
libhwloc 2.11.2 default_h0d58e46_1001 conda-forge
libiconv 1.18 h4ce23a2_1 conda-forge
libidn11 1.34 h1cef754_0 conda-forge
libidn2 2.3.8 ha4ef2c3_0 conda-forge
libjpeg-turbo 3.1.0 hb9d3cd8_0 conda-forge
liblapack 3.9.0 31_h7ac8fdf_openblas conda-forge
libllvm14 14.0.6 hcd5def8_4 conda-forge
liblzma 5.8.1 hb9d3cd8_1 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.29 pthreads_h94d23a6_0 conda-forge
libpng 1.6.47 h943b412_0 conda-forge
libsqlite 3.49.1 hee588c1_2 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 14.2.0 h8f9b012_2 conda-forge
libstdcxx-ng 14.2.0 h4852527_2 conda-forge
libtiff 4.7.0 hd9ff511_4 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
libxml2 2.13.7 h4bc477f_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
llvm-openmp 20.1.4 h024ca30_0 conda-forge
llvmlite 0.43.0 py39hf8b6b1a_1 conda-forge
mafft 7.526 h4bc722e_0 conda-forge
markupsafe 3.0.2 py39h9399b63_1 conda-forge
mash 2.3 hb105d93_9 bioconda
matplotlib-base 3.9.4 py39h16632d1_0 conda-forge
minced 0.4.2 hdfd78af_1 bioconda
mkl 2024.2.2 ha957f24_16 conda-forge
mpfr 4.2.1 h90cbb55_3 conda-forge
mpi 1.0 openmpi conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
narwhals 1.38.0 pyhe01879c_0 conda-forge
ncbi-vdb 3.2.1 h9948957_0 bioconda
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.2.1 pyhd8ed1ab_0 conda-forge
numba 0.60.0 py39h0320e7d_0 conda-forge
numpy 2.0.2 py39h9cb892a_1 conda-forge
openjdk 23.0.2 h53dfc1b_2 conda-forge
openjpeg 2.5.3 h5fbd93e_0 conda-forge
openmpi 4.1.6 hc5af2df_101 conda-forge
openssl 3.5.0 h7b32b05_1 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
panaroo 1.5.2 pyhdfd78af_0 bioconda
parallel 20250422 ha770c72_0 conda-forge
pcre2 10.45 hc749103_0 conda-forge
peewee 3.18.1 py39hf036d5e_0 conda-forge
perl 5.22.2.1 0 conda-forge
perl-archive-tar 2.18 1 bioconda
perl-bioperl 1.6.924 4 bioconda
perl-common-sense 3.74 0 bioconda
perl-exporter-tiny 0.042 1 bioconda
perl-json 2.90 1 bioconda
perl-json-xs 2.34 0 bioconda
perl-list-moreutils 0.413 1 bioconda
perl-threaded 5.32.1 hdfd78af_1 bioconda
perl-xml-namespacesupport 1.11 0 bioconda
perl-xml-parser 2.44 3 bioconda
perl-xml-sax 0.99 0 bioconda
perl-xml-sax-base 1.08 0 bioconda
perl-xml-sax-expat 0.51 0 bioconda
perl-xml-simple 2.22 0 bioconda
perl-yaml 1.24 pl522_1 bioconda
pillow 11.1.0 py39h15c0740_0 conda-forge
pip 25.1.1 pyh8b19718_0 conda-forge
pixman 0.46.0 h29eaf8c_0 conda-forge
plotly 6.0.1 pyhd8ed1ab_0 conda-forge
prank 170427 h9948957_1 bioconda
prodigal 2.6.3 h7b50bb2_10 bioconda
prokka 1.13 2 bioconda
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pyfaidx 0.8.1.4 pyhdfd78af_0 bioconda
pyparsing 3.2.3 pyhd8ed1ab_1 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.9.22 h85ef794_1_cpython conda-forge
python-dateutil 2.9.0.post0 pyhff2d567_1 conda-forge
python-edlib 1.3.9.post1 py39h2de1943_2 bioconda
python-igraph 0.11.8 py39hb479397_0 conda-forge
python_abi 3.9 7_cp39 conda-forge
pyvcf3 1.0.3 pyhdfd78af_0 bioconda
qhull 2020.2 h434a139_5 conda-forge
readline 8.2 h8c095d6_2 conda-forge
requests 2.32.3 pyhd8ed1ab_1 conda-forge
rpsbproc 0.5.0 hd6d6fdc_3 bioconda
scikit-learn 1.6.1 py39h4b7350c_0 conda-forge
scipy 1.13.1 py39haf93ffa_0 conda-forge
setuptools 80.1.0 pyhff2d567_0 conda-forge
simplejson 3.20.1 py39h8cd3c5a_0 conda-forge
six 1.17.0 pyhd8ed1ab_0 conda-forge
taxadb 0.12.1 pyh5e36f6f_0 bioconda
tbb 2021.13.0 hceb3a55_1 conda-forge
tbl2asn 25.7 h9ee0642_1 bioconda
texttable 1.7.0 pyhd8ed1ab_1 conda-forge
threadpoolctl 3.6.0 pyhecae5ae_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
tzdata 2025b h78e105d_0 conda-forge
unicodedata2 16.0.0 py39h8cd3c5a_0 conda-forge
urllib3 2.4.0 pyhd8ed1ab_0 conda-forge
wget 1.21.4 hda4d442_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.12 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-libxrandr 1.5.4 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
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstandard 0.23.0 py39h8cd3c5a_2 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge```
</details>
</br>
Full documentation: https://gtonkinhill.github.io/panaroo/#/
Panaroo is an updated pipeline for pangenome investigation.
[Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G, Lees JA, Gladstone RA, Lo S, Beaudoin C, Floto RA, Frost SDW, Corander J, Bentley SD, Parkhill J. 2020. Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biol 21:180.](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02090-4)
## Example Usage
```bash
# Using GFFs in the same format as output by Prokka run:
mkdir results
panaroo -i *.gff -o results --clean-mode strict