Main tool : Panaroo
Additional tools installed via micromamba:
List of packages in environment: "/opt/conda"
Name Version Build Channel
──────────────────────────────────────────────────────────────────────────────
_openmp_mutex 4.5 20_gnu conda-forge
alsa-lib 1.2.15.3 hb03c661_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 0.12.1 pyhdfd78af_0 bioconda
biopython 1.85 py39h8cd3c5a_1 conda-forge
blast 2.17.0 h66d330f_0 bioconda
brotli 1.2.0 hed03a55_1 conda-forge
brotli-bin 1.2.0 hb03c661_1 conda-forge
brotli-python 1.0.9 py39h5a03fae_8 conda-forge
bzip2 1.0.8 hda65f42_9 conda-forge
c-ares 1.34.6 hb03c661_0 conda-forge
ca-certificates 2026.1.4 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 2025.8.3 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py39h15c3d72_0 conda-forge
charset-normalizer 3.4.3 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
contourpy 1.3.0 py39h74842e3_2 conda-forge
curl 8.18.0 hcf29cc6_1 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
dendropy 5.0.8 pyhdfd78af_1 bioconda
entrez-direct 24.0 he881be0_0 bioconda
expat 2.7.4 hecca717_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 2.17.1 h27c8c51_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 hc364b38_1 conda-forge
fonttools 4.59.1 py39heb7d2ae_0 conda-forge
freetype 2.14.1 ha770c72_0 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 1.3.14 hecca717_2 conda-forge
gsl 2.8 hbf7d49c_1 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
harfbuzz 11.4.5 h15599e2_0 conda-forge
hmmer 3.4 h503566f_3 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 8.7.0 pyhe01879c_1 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 1.5.1 pyhd8ed1ab_0 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
kiwisolver 1.4.7 py39h74842e3_0 conda-forge
krb5 1.22.2 ha1258a1_0 conda-forge
lcms2 2.18 h0c24ade_0 conda-forge
ld_impl_linux-64 2.45.1 default_hbd61a6d_101 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
libasprintf 0.25.1 h3f43e3d_1 conda-forge
libblas 3.11.0 5_h4a7cf45_openblas 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
libcblas 3.11.0 5_h0358290_openblas conda-forge
libcups 2.3.3 h7a8fb5f_6 conda-forge
libcurl 8.18.0 hcf29cc6_1 conda-forge
libdeflate 1.25 h17f619e_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.4 hecca717_0 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libfreetype 2.14.1 ha770c72_0 conda-forge
libfreetype6 2.14.1 h73754d4_0 conda-forge
libgcc 15.2.0 he0feb66_18 conda-forge
libgcc-ng 15.2.0 h69a702a_18 conda-forge
libgettextpo 0.25.1 h3f43e3d_1 conda-forge
libgfortran 15.2.0 h69a702a_18 conda-forge
libgfortran-ng 15.2.0 h69a702a_18 conda-forge
libgfortran5 15.2.0 h68bc16d_18 conda-forge
libglib 2.84.3 hf39c6af_0 conda-forge
libgomp 15.2.0 he0feb66_18 conda-forge
libiconv 1.18 h3b78370_2 conda-forge
libidn11 1.34 h1cef754_0 conda-forge
libidn2 2.3.8 hfac485b_1 conda-forge
libjpeg-turbo 3.1.2 hb03c661_0 conda-forge
liblapack 3.11.0 5_h47877c9_openblas conda-forge
libllvm14 14.0.6 hcd5def8_4 conda-forge
liblzma 5.8.2 hb03c661_0 conda-forge
libnghttp2 1.67.0 had1ee68_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_4 conda-forge
libpng 1.6.55 h421ea60_0 conda-forge
libsqlite 3.51.2 h0c1763c_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.2.0 h934c35e_18 conda-forge
libstdcxx-ng 15.2.0 hdf11a46_18 conda-forge
libtiff 4.7.1 h9d88235_1 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.41.3 h5347b49_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
libxml2 2.13.9 h04c0eec_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 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_10 bioconda
matplotlib-base 3.9.4 py39h16632d1_0 conda-forge
minced 0.4.2 hdfd78af_1 bioconda
mpfr 4.2.1 h90cbb55_3 conda-forge
munkres 1.1.4 pyhd8ed1ab_1 conda-forge
narwhals 2.1.2 pyhe01879c_0 conda-forge
ncbi-vdb 3.3.0 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 24.0.2 h5755bd7_0 conda-forge
openjpeg 2.5.4 h55fea9a_0 conda-forge
openssl 3.6.1 h35e630c_1 conda-forge
packaging 26.0 pyhcf101f3_0 conda-forge
panaroo 1.6.0 pyhdfd78af_0 bioconda
parallel 20260122 ha770c72_0 conda-forge
pcre2 10.45 hc749103_0 conda-forge
peewee 3.18.2 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 11.3.0 py39h15c0740_0 conda-forge
pip 25.2 pyh8b19718_0 conda-forge
pixman 0.46.4 h54a6638_1 conda-forge
plotly 6.3.0 pyhd8ed1ab_0 conda-forge
prank 170427 h9948957_1 bioconda
prodigal 2.6.3 h577a1d6_11 bioconda
prokka 1.13 2 bioconda
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pyfaidx 0.9.0.3 pyhdfd78af_0 bioconda
pyparsing 3.2.3 pyhe01879c_2 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.9.23 hc30ae73_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-edlib 1.3.9.post1 py39h2de1943_2 bioconda
python-igraph 0.11.9 py39h3b801fc_0 conda-forge
python_abi 3.9 8_cp39 conda-forge
pyvcf3 1.0.4 py39hbcbf7aa_0 bioconda
qhull 2020.2 h434a139_5 conda-forge
readline 8.3 h853b02a_0 conda-forge
requests 2.32.5 pyhd8ed1ab_0 conda-forge
scikit-learn 1.6.1 py39h4b7350c_0 conda-forge
scipy 1.13.1 py39haf93ffa_0 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
simplejson 3.20.1 py39h8cd3c5a_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
taxadb 0.12.1 pyh5e36f6f_0 bioconda
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_h366c992_103 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
tzdata 2025c hc9c84f9_1 conda-forge
unicodedata2 16.0.0 py39h8cd3c5a_0 conda-forge
urllib3 2.5.0 pyhd8ed1ab_0 conda-forge
wget 1.25.0 hc2d8bac_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 1.8.13 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 1.8.2 hb9d3cd8_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
zipp 3.23.0 pyhd8ed1ab_0 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstandard 0.23.0 py39hd399759_3 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forge
Full documentation: https://gtonkinhill.github.io/panaroo/#/
Panaroo is an updated pipeline for pangenome investigation.
# Using GFFs in the same format as output by Prokka run:
mkdir results
panaroo -i *.gff -o results --clean-mode strict