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
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 1.86 py312h4c3975b_0 conda-forge
boost-cpp 1.85.0 h3c6214e_4 conda-forge
brotli 1.1.0 hb03c661_4 conda-forge
brotli-bin 1.1.0 hb03c661_4 conda-forge
brotli-python 1.1.0 py312h1289d80_4 conda-forge
bzip2 1.0.8 hda65f42_8 conda-forge
c-ares 1.34.6 hb03c661_0 conda-forge
ca-certificates 2025.11.12 hbd8a1cb_0 conda-forge
certifi 2025.11.12 pyhd8ed1ab_0 conda-forge
cffi 2.0.0 py312h460c074_1 conda-forge
charset-normalizer 3.4.4 pyhd8ed1ab_0 conda-forge
clarabel 0.11.1 py312h6b5fed6_1 conda-forge
click 8.3.1 pyh8f84b5b_1 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
contourpy 1.3.3 py312hd9148b4_3 conda-forge
cvxpy 1.7.5 py312h7900ff3_0 conda-forge
cvxpy-base 1.7.5 py312hf79963d_0 conda-forge
cycler 0.12.1 pyhcf101f3_2 conda-forge
docutils 0.21.2 pyhd8ed1ab_1 conda-forge
epiweeks 2.3.0 pyhdfd78af_0 bioconda
fonttools 4.61.1 py312h8a5da7c_0 conda-forge
freetype 2.14.1 ha770c72_0 conda-forge
freyja 2.0.2 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 3.11 pyhd8ed1ab_0 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 pyhcf101f3_1 conda-forge
joblib 1.5.3 pyhd8ed1ab_0 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
kiwisolver 1.4.9 py312h0a2e395_2 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.17 h717163a_0 conda-forge
ld_impl_linux-64 2.45 default_hbd61a6d_104 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
libabseil 20240116.2 cxx17_he02047a_1 conda-forge
libarrow 17.0.0 had3b6fe_16_cpu conda-forge
libarrow-acero 17.0.0 h5888daf_16_cpu conda-forge
libarrow-dataset 17.0.0 h5888daf_16_cpu conda-forge
libarrow-substrait 17.0.0 hf54134d_16_cpu conda-forge
libasprintf 0.25.1 h3f43e3d_1 conda-forge
libblas 3.11.0 5_h4a7cf45_openblas conda-forge
libboost 1.85.0 h0ccab89_4 conda-forge
libboost-devel 1.85.0 h00ab1b0_4 conda-forge
libboost-headers 1.85.0 ha770c72_4 conda-forge
libbrotlicommon 1.1.0 hb03c661_4 conda-forge
libbrotlidec 1.1.0 hb03c661_4 conda-forge
libbrotlienc 1.1.0 hb03c661_4 conda-forge
libcblas 3.11.0 5_h0358290_openblas conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcurl 8.17.0 h4e3cde8_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
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.7.3 hecca717_0 conda-forge
libffi 3.5.2 h9ec8514_0 conda-forge
libfreetype 2.14.1 ha770c72_0 conda-forge
libfreetype6 2.14.1 h73754d4_0 conda-forge
libgcc 15.2.0 he0feb66_16 conda-forge
libgcc-ng 15.2.0 h69a702a_16 conda-forge
libgettextpo 0.25.1 h3f43e3d_1 conda-forge
libgfortran 15.2.0 h69a702a_16 conda-forge
libgfortran-ng 15.2.0 h69a702a_16 conda-forge
libgfortran5 15.2.0 h68bc16d_16 conda-forge
libgomp 15.2.0 he0feb66_16 conda-forge
libgoogle-cloud 2.29.0 h435de7b_0 conda-forge
libgoogle-cloud-storage 2.29.0 h0121fbd_0 conda-forge
libgrpc 1.62.2 h15f2491_0 conda-forge
libiconv 1.18 h3b78370_2 conda-forge
libjpeg-turbo 3.1.2 hb03c661_0 conda-forge
liblapack 3.11.0 5_h47877c9_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
liblzma-devel 5.8.1 hb9d3cd8_2 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
libopenssl-static 3.6.0 hb03c661_0 conda-forge
libosqp 1.0.0 np2py312h1a77e3e_2 conda-forge
libparquet 17.0.0 h39682fd_16_cpu conda-forge
libpng 1.6.53 h421ea60_0 conda-forge
libprotobuf 4.25.3 hd5b35b9_1 conda-forge
libqdldl 0.1.8 h3f2d84a_1 conda-forge
libre2-11 2023.09.01 h5a48ba9_2 conda-forge
libsqlite 3.51.1 h0c1763c_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.2.0 h934c35e_16 conda-forge
libstdcxx-ng 15.2.0 hdf11a46_16 conda-forge
libthrift 0.20.0 h0e7cc3e_1 conda-forge
libtiff 4.7.1 h9d88235_1 conda-forge
libutf8proc 2.8.0 hf23e847_1 conda-forge
libuuid 2.41.2 h5347b49_1 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
lz4-c 1.9.4 hcb278e6_0 conda-forge
mafft 7.526 h4bc722e_0 conda-forge
markupsafe 3.0.3 py312h8a5da7c_0 conda-forge
matplotlib-base 3.10.8 py312he3d6523_0 conda-forge
mpfr 4.2.1 h90cbb55_3 conda-forge
mpi 1.0 openmpi conda-forge
munkres 1.1.4 pyhd8ed1ab_1 conda-forge
mysql-connector-c 6.1.11 h659d440_1008 conda-forge
narwhals 2.14.0 pyhcf101f3_0 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
numpy 2.3.5 py312h33ff503_0 conda-forge
openjpeg 2.5.4 h55fea9a_0 conda-forge
openmpi 4.1.6 hc5af2df_101 conda-forge
openssl 3.6.0 h26f9b46_0 conda-forge
orc 2.0.2 h669347b_0 conda-forge
osqp 1.0.5 np2py312h0f77346_4 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.3.3 py312hf79963d_1 conda-forge
pillow 12.0.0 py312h50c33e8_2 conda-forge
pip 25.3 pyh8b19718_0 conda-forge
plotly 6.5.0 pyhd8ed1ab_0 conda-forge
protobuf 4.25.3 py312h83439f5_1 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pyarrow 17.0.0 py312h9cebb41_2 conda-forge
pyarrow-core 17.0.0 py312h01725c0_2_cpu conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pygments 2.19.2 pyhd8ed1ab_0 conda-forge
pyparsing 3.2.5 pyhcf101f3_0 conda-forge
pysam 0.23.3 py312h47d5410_1 bioconda
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.12.12 hd63d673_1_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-tzdata 2025.3 pyhd8ed1ab_0 conda-forge
python_abi 3.12 8_cp312 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.3 py312h8a5da7c_0 conda-forge
qdldl-python 0.1.7.post5 np2py312h0f77346_3 conda-forge
qhull 2020.2 h434a139_5 conda-forge
re2 2023.09.01 h7f4b329_2 conda-forge
readline 8.3 h853b02a_0 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 1.16.3 py312h7a1785b_1 conda-forge
scs 3.2.9 default_py312he8c76e8_1 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_1 conda-forge
snowballstemmer 3.0.1 pyhd8ed1ab_0 conda-forge
sphinx 8.2.3 pyhd8ed1ab_0 conda-forge
sphinx-click 6.2.0 pyhcf101f3_0 conda-forge
sphinx_rtd_theme 3.0.2 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 2020.2 h4bd325d_4 conda-forge
tbb-devel 2020.2 h4bd325d_4 conda-forge
tk 8.6.13 noxft_ha0e22de_103 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
tzdata 2025c h8577fbf_0 conda-forge
ucsc-fatovcf 482 hdc0a859_1 bioconda
unicodedata2 17.0.0 py312h4c3975b_1 conda-forge
urllib3 2.5.0 pyhd8ed1ab_0 conda-forge
usher 0.6.6 hdd55de9_4 bioconda
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
xorg-libxau 1.0.12 hb03c661_1 conda-forge
xorg-libxdmcp 1.1.5 hb03c661_1 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
zlib-ng 2.3.2 h54a6638_0 conda-forge
zstandard 0.25.0 py312h5253ce2_1 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forge
This docker image was built on 2025-12-16 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 12_16_2025-00-37 as reported by freyja demix --version --pathogen SARS-CoV-2
This image is rebuilt every week on Dockerhub and Quay.io with the tag ${{ base FREYJA version }}-${{ pathogen }}-${{ FREYJA database version }}-${{ date the 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.