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:
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
arrow-cpp 11.0.0 ha770c72_12_cpu conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
aws-c-auth 0.6.26 h987a71b_2 conda-forge
aws-c-cal 0.5.21 h48707d8_2 conda-forge
aws-c-common 0.8.14 h0b41bf4_0 conda-forge
aws-c-compression 0.2.16 h03acc5a_5 conda-forge
aws-c-event-stream 0.2.20 h00877a2_4 conda-forge
aws-c-http 0.7.6 hf342b9f_0 conda-forge
aws-c-io 0.13.19 h5b20300_3 conda-forge
aws-c-mqtt 0.8.6 hc4349f7_12 conda-forge
aws-c-s3 0.2.7 h909e904_1 conda-forge
aws-c-sdkutils 0.1.9 h03acc5a_0 conda-forge
aws-checksums 0.1.14 h03acc5a_5 conda-forge
aws-crt-cpp 0.19.8 hf7fbfca_12 conda-forge
aws-sdk-cpp 1.10.57 h17c43bd_8 conda-forge
babel 2.17.0 pyhd8ed1ab_0 conda-forge
biopython 1.85 py311h9ecbd09_1 conda-forge
boost-cpp 1.78.0 h2c5509c_4 conda-forge
brotli 1.0.9 h166bdaf_9 conda-forge
brotli-bin 1.0.9 h166bdaf_9 conda-forge
brotli-python 1.0.9 py311ha362b79_9 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
clarabel 0.11.1 py311heb70b45_0 conda-forge
click 8.2.1 pyh707e725_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
contourpy 1.3.2 py311hd18a35c_0 conda-forge
cvxpy 1.7.1 py311h38be061_0 conda-forge
cvxpy-base 1.7.1 py311hed34c8f_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 4.59.0 py311h3778330_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
freyja 2.0.0 py311h9ee0642_0 bioconda
gawk 5.3.1 hcd3d067_0 conda-forge
gflags 2.2.2 h5888daf_1005 conda-forge
glog 0.6.0 h6f12383_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
htslib 1.21 h5efdd21_0 bioconda
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 73.2 h59595ed_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 1.4.3 h43eeafb_0 bioconda
jinja2 3.1.6 pyhd8ed1ab_0 conda-forge
joblib 1.5.1 pyhd8ed1ab_0 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 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.44 h1423503_1 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
libabseil 20230125.0 cxx17_hcb278e6_1 conda-forge
libarrow 11.0.0 h51ec05e_12_cpu conda-forge
libasprintf 0.25.1 h8e693c7_0 conda-forge
libblas 3.9.0 32_h59b9bed_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_9 conda-forge
libbrotlidec 1.0.9 h166bdaf_9 conda-forge
libbrotlienc 1.0.9 h166bdaf_9 conda-forge
libcap 2.75 h39aace5_0 conda-forge
libcblas 3.9.0 32_he106b2a_openblas conda-forge
libcbor 0.10.2 hcb278e6_0 conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcurl 8.8.0 hca28451_1 conda-forge
libdeflate 1.20 hd590300_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 2.7.1 hecca717_0 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libfido2 1.14.0 h4446dcb_0 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
libgoogle-cloud 2.8.0 h0bc5f78_1 conda-forge
libgrpc 1.52.1 hcf146ea_1 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
liblzma-devel 5.8.1 hb9d3cd8_2 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_0 conda-forge
libopenssl-static 3.5.1 hb9d3cd8_0 conda-forge
libosqp 0.6.3 h5888daf_1 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libprotobuf 3.21.12 hfc55251_2 conda-forge
libqdldl 0.1.7 hcb278e6_0 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx 15.1.0 h8f9b012_3 conda-forge
libstdcxx-ng 15.1.0 h4852527_3 conda-forge
libthrift 0.18.1 h8fd135c_2 conda-forge
libtiff 4.6.0 h1dd3fc0_3 conda-forge
libudev1 257.7 hbe16f8c_0 conda-forge
libutf8proc 2.8.0 hf23e847_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.6.0 hd42ef1d_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.2.13 h4ab18f5_6 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
mafft 7.526 h4bc722e_0 conda-forge
markupsafe 3.0.2 py311h2dc5d0c_1 conda-forge
matplotlib-base 3.10.1 py311h2b939e6_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 1.48.0 pyhe01879c_0 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
numpy 1.26.4 py311h64a7726_0 conda-forge
openjpeg 2.5.2 h488ebb8_0 conda-forge
openmpi 4.1.2 hbfc84c5_0 conda-forge
openssh 9.6p1 h2d3b35a_0 conda-forge
openssl 3.5.1 h7b32b05_0 conda-forge
orc 1.8.3 h2f23424_1 conda-forge
osqp 0.6.7.post3 py311h7db5c69_1 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.3.1 py311hed34c8f_0 conda-forge
parquet-cpp 1.5.1 2 conda-forge
pillow 10.3.0 py311h18e6fac_0 conda-forge
pip 25.1.1 pyh8b19718_0 conda-forge
plotly 6.2.0 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pyarrow 11.0.0 py311hbdf6286_12_cpu conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pygments 2.19.2 pyhd8ed1ab_0 conda-forge
pyparsing 3.2.3 pyhd8ed1ab_1 conda-forge
pysam 0.22.1 py311h1f0e11c_2 bioconda
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.11.9 hb806964_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_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
qdldl-python 0.1.7.post5 np20py311h31610b7_1 conda-forge
qhull 2020.2 h434a139_5 conda-forge
re2 2023.02.02 hcb278e6_0 conda-forge
readline 8.2 h8c095d6_2 conda-forge
requests 2.32.4 pyhd8ed1ab_0 conda-forge
roman-numerals-py 3.1.0 pyhd8ed1ab_0 conda-forge
s2n 1.3.41 h3358134_0 conda-forge
samtools 1.21 h50ea8bc_0 bioconda
scipy 1.16.0 py311h2d3ef60_0 conda-forge
scs 3.2.7.post2 default_py311he11e7d9_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 1.1.10 hdb0a2a9_1 conda-forge
snowballstemmer 3.0.1 pyhd8ed1ab_0 conda-forge
sphinx 8.2.3 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
tk 8.6.13 noxft_h4845f30_101 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
tzdata 2025b h78e105d_0 conda-forge
ucsc-fatovcf 473 he8037a5_0 bioconda
ucsc-stringify 472 he8037a5_0 bioconda
unicodedata2 16.0.0 py311h9ecbd09_0 conda-forge
urllib3 2.5.0 pyhd8ed1ab_0 conda-forge
usher 0.6.3 hb389108_1 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 h7f98852_2 conda-forge
zlib 1.2.13 h4ab18f5_6 conda-forge
zstandard 0.23.0 py311h9ecbd09_2 conda-forge
zstd 1.5.6 ha6fb4c9_0 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 07_21_2025-00-46 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.