Main tool: bakta
Additional tools installed via micromamba:
Name Version Build Channel
────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
about-time 4.2.1 pyhd8ed1ab_1 conda-forge
alive-progress 3.0.1 pyhd8ed1ab_0 conda-forge
aragorn 1.2.41 h7b50bb2_5 bioconda
archspec 0.2.5 pyhd8ed1ab_0 conda-forge
backports.zstd 1.3.0 py313h18e8e13_0 conda-forge
bakta 1.12.0 pyhdfd78af_0 bioconda
biopython 1.86 py313h07c4f96_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 1.2.0 py313hf159716_1 conda-forge
bzip2 1.0.8 hda65f42_8 conda-forge
c-ares 1.34.6 hb03c661_0 conda-forge
ca-certificates 2026.1.4 hbd8a1cb_0 conda-forge
certifi 2026.1.4 pyhd8ed1ab_0 conda-forge
cffi 2.0.0 py313hf46b229_1 conda-forge
charset-normalizer 3.4.4 pyhd8ed1ab_0 conda-forge
contourpy 1.3.3 py313hc8edb43_4 conda-forge
curl 8.18.0 h4e3cde8_0 conda-forge
cycler 0.12.1 pyhcf101f3_2 conda-forge
diamond 2.1.22 h13889ed_0 bioconda
entrez-direct 24.0 he881be0_0 bioconda
fonttools 4.61.1 py313h3dea7bd_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
libzlib 1.3.1 hb9d3cd8_2 conda-forge
matplotlib-base 3.10.8 py313h683a580_0 conda-forge
mpi 1.0 openmpi conda-forge
munkres 1.1.4 pyhd8ed1ab_1 conda-forge
ncbi-amrfinderplus 4.2.7 hf69ffd2_0 bioconda
ncbi-vdb 3.3.0 h9948957_0 bioconda
ncurses 6.5 h2d0b736_3 conda-forge
numpy 2.4.2 py313hf6604e3_1 conda-forge
openjpeg 2.5.4 h55fea9a_0 conda-forge
openmpi 4.1.6 hc5af2df_101 conda-forge
openssl 3.6.1 h35e630c_1 conda-forge
packaging 26.0 pyhcf101f3_0 conda-forge
pandas 3.0.0 py313hbfd7664_0 conda-forge
pbzip2 1.1.13 h1fcc475_2 conda-forge
pcre2 10.45 hc749103_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
perl-archive-tar 3.04 pl5321hdfd78af_0 bioconda
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-common-sense 3.75 pl5321hd8ed1ab_0 conda-forge
perl-compress-raw-bzip2 2.214 pl5321hda65f42_0 conda-forge
perl-compress-raw-zlib 2.214 pl5321h4dac143_0 conda-forge
perl-encode 3.21 pl5321hb9d3cd8_1 conda-forge
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0 conda-forge
perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge
perl-io-compress 2.216 pl5321h503566f_0 bioconda
perl-io-zlib 1.15 pl5321hdfd78af_1 bioconda
perl-json 4.10 pl5321hdfd78af_1 bioconda
perl-json-xs 4.04 pl5321h9948957_0 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h7b50bb2_5 bioconda
perl-parent 0.243 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321hb9d3cd8_2 conda-forge
perl-scalar-list-utils 1.70 pl5321hb03c661_0 conda-forge
perl-storable 3.15 pl5321hb9d3cd8_2 conda-forge
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
pigz 2.8 h421ea60_2 conda-forge
piler-cr 1.06 h9948957_6 bioconda
pillow 12.1.0 py313h80991f8_0 conda-forge
pip 26.0.1 pyh145f28c_0 conda-forge
psutil 7.2.2 py313h54dd161_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pycirclize 1.10.1 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pyhmmer 0.12.0 py313h366bbf7_0 bioconda
pyparsing 3.3.2 pyhcf101f3_0 conda-forge
pyrodigal 3.7.0 py313h366bbf7_0 bioconda
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.13.12 hc97d973_100_cp313 conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-isal 1.8.0 py313h07c4f96_1 conda-forge
python-zlib-ng 1.0.0 py313ha345abf_1 conda-forge
python_abi 3.13 8_cp313 conda-forge
pyyaml 6.0.3 py313h3dea7bd_1 conda-forge
qhull 2020.2 h434a139_5 conda-forge
readline 8.3 h853b02a_0 conda-forge
requests 2.32.5 pyhcf101f3_1 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
tk 8.6.13 noxft_h366c992_103 conda-forge
trnascan-se 2.0.12 pl5321h7b50bb2_2 bioconda
tzdata 2025c hc9c84f9_1 conda-forge
urllib3 2.6.3 pyhd8ed1ab_0 conda-forge
wget 1.25.0 hc2d8bac_0 conda-forge
xopen 2.0.2 pyh707e725_2 conda-forge
xorg-libxau 1.0.12 hb03c661_1 conda-forge
xorg-libxdmcp 1.1.5 hb03c661_1 conda-forge
yaml 0.2.5 h280c20c_3 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zlib-ng 2.3.3 hceb46e0_1 conda-forge
zstandard 0.25.0 py313h54dd161_1 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forge
Code repository: https://github.com/oschwengers/bakta
Basic information on how to use this tool:
- executable: bakta
- help: -h
- version: -v
- description: Annotates bacterial genomes
Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations in machine-readable JSON & bioinformatics standard file formats for automated downstream analysis.
Additional information:
WARNING : Image does not contain a database.
Full documentation: https://github.com/oschwengers/bakta/
bakta sample.fasta --db <path to database> --threads 20 --prefix sample