Main tool: bakta
Additional tools installed via micromamba:
List of packages in environment: "/opt/conda"
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
bakta 1.11.3 pyhdfd78af_0 bioconda
biopython 1.85 py311h9ecbd09_1 conda-forge
blast 2.16.0 h66d330f_5 bioconda
brotli 1.1.0 hb9d3cd8_3 conda-forge
brotli-bin 1.1.0 hb9d3cd8_3 conda-forge
brotli-python 1.1.0 py311hfdbb021_3 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.7.14 hbd8a1cb_0 conda-forge
certifi 2025.7.14 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py311hf29c0ef_0 conda-forge
charset-normalizer 3.4.2 pyhd8ed1ab_0 conda-forge
contourpy 1.3.2 py311hd18a35c_0 conda-forge
curl 8.14.1 h332b0f4_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
diamond 2.1.12 h13889ed_3 bioconda
entrez-direct 22.4 he881be0_0 bioconda
fonttools 4.59.0 py311h3778330_0 conda-forge
freetype 2.13.3 ha770c72_1 conda-forge
grapheme 0.6.0 pyhd8ed1ab_1 conda-forge
gsl 2.7 he838d99_0 conda-forge
h2 4.2.0 pyhd8ed1ab_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
infernal 1.1.5 pl5321h7b50bb2_4 bioconda
isa-l 2.31.1 hb9d3cd8_1 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.8 py311hd18a35c_1 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.17 h717163a_0 conda-forge
ld_impl_linux-64 2.44 h1423503_1 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
libasprintf 0.25.1 h8e693c7_0 conda-forge
libblas 3.9.0 32_h59b9bed_openblas conda-forge
libbrotlicommon 1.1.0 hb9d3cd8_3 conda-forge
libbrotlidec 1.1.0 hb9d3cd8_3 conda-forge
libbrotlienc 1.1.0 hb9d3cd8_3 conda-forge
libcblas 3.9.0 32_he106b2a_openblas conda-forge
libcurl 8.14.1 h332b0f4_0 conda-forge
libdeflate 1.24 h86f0d12_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.1 hecca717_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 15.1.0 h767d61c_3 conda-forge
libgcc-ng 15.1.0 h69a702a_3 conda-forge
libgettextpo 0.25.1 h5888daf_0 conda-forge
libgfortran 15.1.0 h69a702a_3 conda-forge
libgfortran-ng 15.1.0 h69a702a_3 conda-forge
libgfortran5 15.1.0 hcea5267_3 conda-forge
libgomp 15.1.0 h767d61c_3 conda-forge
libidn2 2.3.8 ha4ef2c3_0 conda-forge
libjpeg-turbo 3.1.0 hb9d3cd8_0 conda-forge
liblapack 3.9.0 32_h7ac8fdf_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_0 conda-forge
libpng 1.6.50 h943b412_0 conda-forge
libsqlite 3.50.3 hee844dc_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.1.0 h8f9b012_3 conda-forge
libstdcxx-ng 15.1.0 h4852527_3 conda-forge
libtiff 4.7.0 hf01ce69_5 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_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 3.10.3 py311h2b939e6_0 conda-forge
mpi 1.0 openmpi conda-forge
munkres 1.1.4 pyhd8ed1ab_1 conda-forge
ncbi-amrfinderplus 4.0.23 hf69ffd2_0 bioconda
ncbi-vdb 3.2.1 h9948957_0 bioconda
ncurses 6.5 h2d0b736_3 conda-forge
numpy 2.3.1 py311h2e04523_1 conda-forge
openjpeg 2.5.3 h5fbd93e_0 conda-forge
openmpi 4.1.6 hc5af2df_101 conda-forge
openssl 3.5.1 h7b32b05_0 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.3.1 py311hed34c8f_0 conda-forge
pbzip2 1.1.13 h1fcc475_2 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 2.201 pl5321hbf60520_1 conda-forge
perl-compress-raw-zlib 2.202 pl5321hadc24fc_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 2.201 pl5321h503566f_5 bioconda
perl-io-zlib 1.15 pl5321hdfd78af_1 bioconda
perl-json 4.10 pl5321hdfd78af_1 bioconda
perl-json-xs 4.03 pl5321h9948957_4 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 1.69 pl5321hb9d3cd8_0 conda-forge
perl-storable 3.15 pl5321hb9d3cd8_2 conda-forge
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
pigz 2.8 hadc24fc_1 conda-forge
piler-cr 1.06 h9948957_6 bioconda
pillow 11.3.0 py311h1322bbf_0 conda-forge
pip 25.1.1 pyh8b19718_0 conda-forge
psutil 7.0.0 py311h9ecbd09_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pycirclize 1.9.1 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pyhmmer 0.11.1 py311haab0aaa_2 bioconda
pyparsing 3.2.3 pyhd8ed1ab_1 conda-forge
pyrodigal 3.6.3.post1 py311haab0aaa_1 bioconda
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.11.13 h9e4cc4f_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-isal 1.7.2 py311h9ecbd09_0 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python-zlib-ng 0.5.1 py311h1a83624_0 conda-forge
python_abi 3.11 8_cp311 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py311h2dc5d0c_2 conda-forge
qhull 2020.2 h434a139_5 conda-forge
readline 8.2 h8c095d6_2 conda-forge
requests 2.32.4 pyhd8ed1ab_0 conda-forge
rpsbproc 0.5.0 hd6d6fdc_3 bioconda
setuptools 80.9.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
tk 8.6.13 noxft_hd72426e_102 conda-forge
trnascan-se 2.0.12 pl5321h7b50bb2_2 bioconda
tzdata 2025b h78e105d_0 conda-forge
unicodedata2 16.0.0 py311h9ecbd09_0 conda-forge
urllib3 2.5.0 pyhd8ed1ab_0 conda-forge
wget 1.21.4 hda4d442_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
xopen 2.0.2 pyh707e725_2 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zlib-ng 2.2.4 h7955e40_0 conda-forge
zstandard 0.23.0 py311h9ecbd09_2 conda-forge
zstd 1.5.7 hb8e6e7a_2 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