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 1.2.16.1 hb03c661_0 conda-forge
any2fasta 0.8.1 hdfd78af_0 bioconda
aragorn 1.2.41 h7b50bb2_5 bioconda
archspec 0.2.5 pyhd8ed1ab_0 conda-forge
argcomplete 3.6.2 pyhd8ed1ab_0 conda-forge
argh 0.31.3 pyhd8ed1ab_1 conda-forge
argtable2 2.13 hd590300_1004 conda-forge
aria2 1.37.0 h4e1c2bf_3 conda-forge
arpack 3.9.1 nompi_hf03ea27_102 conda-forge
barrnap 1.10.6 pl5321hdfd78af_0 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
blast-legacy 2.2.26 hf7ff83a_5 bioconda
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
xz 5.8.3 ha02ee65_0 conda-forge
xz-gpl-tools 5.8.3 ha02ee65_0 conda-forge
xz-tools 5.8.3 hb03c661_0 conda-forge
ziggypep 0.3.1 hdfd78af_0 bioconda
zipp 3.23.0 pyhd8ed1ab_0 conda-forge
zlib 1.3.2 h25fd6f3_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