Main tool & documentation: freyja
Freyja is a tool to recover relative lineage abundances from mixed samples from a sequencing dataset . The method uses lineage-determining mutational "barcodes" derived from the UShER global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem.
Additional tools installed via micromamba:
List of packages in environment: "/opt/conda/envs/freyja-env"
Name Version Build Channel
────────────────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alabaster 1.0.0 pyhd8ed1ab_1 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
aws-c-auth 0.7.31 he1a10d6_2 conda-forge
aws-c-cal 0.7.4 hae4d56a_2 conda-forge
aws-c-common 0.9.29 hb9d3cd8_0 conda-forge
aws-c-compression 0.2.19 h2bff981_2 conda-forge
aws-c-event-stream 0.4.3 h19b0707_4 conda-forge
aws-c-http 0.8.10 h14a7884_2 conda-forge
aws-c-io 0.14.19 hc9e6898_1 conda-forge
aws-c-mqtt 0.10.7 hb8d5873_2 conda-forge
aws-c-s3 0.6.7 h666547d_0 conda-forge
aws-c-sdkutils 0.1.19 h2bff981_4 conda-forge
aws-checksums 0.1.20 h2bff981_1 conda-forge
aws-crt-cpp 0.28.3 hbe26082_8 conda-forge
aws-sdk-cpp 1.11.407 h25d6d5c_1 conda-forge
azure-core-cpp 1.13.0 h935415a_0 conda-forge
azure-identity-cpp 1.8.0 hd126650_2 conda-forge
azure-storage-blobs-cpp 12.12.0 hd2e3451_0 conda-forge
azure-storage-common-cpp 12.7.0 h10ac4d7_1 conda-forge
azure-storage-files-datalake-cpp 12.11.0 h325d260_1 conda-forge
babel 2.17.0 pyhd8ed1ab_0 conda-forge
biopython 1.85 py312h66e93f0_1 conda-forge
boost-cpp 1.85.0 h3c6214e_4 conda-forge
brotli 1.1.0 hb9d3cd8_3 conda-forge
brotli-bin 1.1.0 hb9d3cd8_3 conda-forge
brotli-python 1.1.0 py312h2ec8cdc_3 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.8.3 hbd8a1cb_0 conda-forge
certifi 2025.8.3 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py312h06ac9bb_0 conda-forge
charset-normalizer 3.4.3 pyhd8ed1ab_0 conda-forge
clarabel 0.11.1 py312h407087e_0 conda-forge
click 8.2.1 pyh707e725_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
contourpy 1.3.3 py312hd9148b4_1 conda-forge
cvxpy 1.7.2 py312h7900ff3_0 conda-forge
cvxpy-base 1.7.2 py312hf79963d_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
docutils 0.21.2 pyhd8ed1ab_1 conda-forge
epiweeks 2.3.0 pyhdfd78af_0 bioconda
fonttools 4.59.2 py312h8a5da7c_0 conda-forge
freetype 2.13.3 ha770c72_1 conda-forge
freyja 2.0.1 pyhdfd78af_0 bioconda
gawk 5.3.1 hcd3d067_0 conda-forge
gflags 2.2.2 h5888daf_1005 conda-forge
glog 0.7.1 hbabe93e_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
h2 4.3.0 pyhcf101f3_0 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
htslib 1.22.1 h566b1c6_0 bioconda
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
imagesize 1.4.1 pyhd8ed1ab_0 conda-forge
isa-l 2.31.1 hb9d3cd8_1 conda-forge
ivar 1.4.4 h077b44d_0 bioconda
jinja2 3.1.6 pyhd8ed1ab_0 conda-forge
joblib 1.5.2 pyhd8ed1ab_0 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
kiwisolver 1.4.9 py312h0a2e395_0 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
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python_abi 3.12 8_cp312 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py312h178313f_2 conda-forge
qdldl-python 0.1.7.post5 np20py312h6792212_1 conda-forge
qhull 2020.2 h434a139_5 conda-forge
re2 2023.09.01 h7f4b329_2 conda-forge
readline 8.2 h8c095d6_2 conda-forge
requests 2.32.5 pyhd8ed1ab_0 conda-forge
roman-numerals-py 3.1.0 pyhd8ed1ab_0 conda-forge
s2n 1.5.5 h3931f03_0 conda-forge
samtools 1.22.1 h96c455f_0 bioconda
scipy 1.16.1 py312h4ebe9ca_0 conda-forge
scs 3.2.7.post2 default_py312hfaafd5f_0 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_3 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
snappy 1.2.2 h03e3b7b_0 conda-forge
snowballstemmer 3.0.1 pyhd8ed1ab_0 conda-forge
sphinx 8.3.0 pyhd8ed1ab_0 conda-forge
sphinx-click 6.0.0 pyhd8ed1ab_1 conda-forge
sphinx_rtd_theme 3.0.1 pyha770c72_0 conda-forge
sphinxcontrib-applehelp 2.0.0 pyhd8ed1ab_1 conda-forge
sphinxcontrib-devhelp 2.0.0 pyhd8ed1ab_1 conda-forge
sphinxcontrib-htmlhelp 2.1.0 pyhd8ed1ab_1 conda-forge
sphinxcontrib-jquery 4.1 pyhd8ed1ab_1 conda-forge
sphinxcontrib-jsmath 1.0.1 pyhd8ed1ab_1 conda-forge
sphinxcontrib-qthelp 2.0.0 pyhd8ed1ab_1 conda-forge
sphinxcontrib-serializinghtml 1.1.10 pyhd8ed1ab_1 conda-forge
tbb 2022.2.0 hb60516a_1 conda-forge
tbb-devel 2022.2.0 h74b38a2_1 conda-forge
tk 8.6.13 noxft_hd72426e_102 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
tzdata 2025b h78e105d_0 conda-forge
ucsc-fatovcf 482 hdc0a859_1 bioconda
unicodedata2 16.0.0 py312h66e93f0_0 conda-forge
urllib3 2.5.0 pyhd8ed1ab_0 conda-forge
usher 0.6.6 h719ac0c_2 bioconda
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xz 5.8.1 hbcc6ac9_2 conda-forge
xz-gpl-tools 5.8.1 hbcc6ac9_2 conda-forge
xz-tools 5.8.1 hb9d3cd8_2 conda-forge
yaml 0.2.5 h280c20c_3 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstandard 0.23.0 py312h4c3975b_3 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge
This docker image was built on 2025-07-22 and the command freyja update is run as part of the build to retrieve the most up-to-date database. The barcode version included in this docker image is 08_28_2025-00-33 as reported by freyja demix --version
This image is rebuilt every week on Dockerhub and Quay.io with the tag ${freyja version}-${freyja database version}-${data image was deployed}.
# run freyja variants to call variants from an aligned SC2 bam file
freyja variants [bamfile] --variants [variant outfile name] --depths [depths outfile name] --ref [reference.fa]
# run freyja demix to identify lineages based on called variants
freyja demix [variants-file] [depth-file] --output [output-file]Warning: freyja update does not work under all conditions. You may need to specify an output directory (freyja update --outdir /path/to/outdir) for which your user has write privileges, such as a mounted volume.