Main tool: clair3
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
abseil-cpp 20210324.2 h9c3ff4c_0 conda-forge
absl-py 2.2.0 pyhd8ed1ab_0 conda-forge
aiohappyeyeballs 2.6.1 pyhd8ed1ab_0 conda-forge
aiohttp 3.11.18 py39h9399b63_0 conda-forge
aiosignal 1.3.2 pyhd8ed1ab_0 conda-forge
amply 0.1.6 pyhd8ed1ab_1 conda-forge
astunparse 1.6.3 pyhd8ed1ab_3 conda-forge
async-timeout 5.0.1 pyhd8ed1ab_1 conda-forge
attrs 25.3.0 pyh71513ae_0 conda-forge
biopython 1.85 py39h8cd3c5a_1 conda-forge
blinker 1.9.0 pyhff2d567_0 conda-forge
blosc 1.21.5 h0f2a231_0 conda-forge
brotli-python 1.1.0 py39hf88036b_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
c-blosc2 2.12.0 hb4ffafa_0 conda-forge
ca-certificates 2025.4.26 hbd8a1cb_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.5.2 pyhd8ed1ab_0 conda-forge
certifi 2025.1.31 pyhd8ed1ab_0 conda-forge
cffi 1.14.4 py39he88106c_0 conda-forge
charset-normalizer 3.4.2 pyhd8ed1ab_0 conda-forge
click 8.1.8 pyh707e725_0 conda-forge
coin-or-cbc 2.10.12 h8b142ea_1 conda-forge
coin-or-cgl 0.60.7 h516709c_0 conda-forge
coin-or-clp 1.17.8 h1ee7a9c_0 conda-forge
coin-or-osi 0.108.10 haf5fa05_0 conda-forge
coin-or-utils 2.11.11 hee58242_0 conda-forge
coincbc 2.10.12 2_metapackage conda-forge
cryptography 39.0.0 py39hd598818_0 conda-forge
docutils 0.21.2 pyhd8ed1ab_1 conda-forge
expat 2.7.0 h5888daf_0 conda-forge
frozenlist 1.5.0 py39h9399b63_1 conda-forge
gast 0.6.0 pyhd8ed1ab_0 conda-forge
gdbm 1.18 h0a1914f_2 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
google-auth 2.40.0 pyhd8ed1ab_0 conda-forge
google-auth-oauthlib 0.4.6 pyhd8ed1ab_0 conda-forge
google-pasta 0.2.0 pyhd8ed1ab_2 conda-forge
grpc-cpp 1.43.2 h9e046d8_3 conda-forge
grpcio 1.43.0 py39hff7568b_0 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
h5py 3.9.0 nompi_py39h4dfffb9_100 conda-forge
hdf5 1.14.0 nompi_h5231ba7_103 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
htslib 1.17 h6bc39ce_1 bioconda
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 70.1 h27087fc_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
importlib-metadata 8.6.1 pyha770c72_0 conda-forge
isa-l 2.31.1 hb9d3cd8_1 conda-forge
jpeg 9e h0b41bf4_3 conda-forge
keras 2.8.0 pyhd8ed1ab_0 conda-forge
keras-preprocessing 1.1.2 pyhd8ed1ab_1 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.20.1 hf9c8cef_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libblas 3.9.0 31_h59b9bed_openblas conda-forge
libcblas 3.9.0 31_he106b2a_openblas conda-forge
libcurl 7.87.0 h6312ad2_0 conda-forge
libdeflate 1.23 h86f0d12_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.0 h5888daf_0 conda-forge
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc 14.2.0 h767d61c_2 conda-forge
libgcc-ng 14.2.0 h69a702a_2 conda-forge
libgfortran 14.2.0 h69a702a_2 conda-forge
libgfortran-ng 14.2.0 h69a702a_2 conda-forge
libgfortran5 14.2.0 hf1ad2bd_2 conda-forge
libgomp 14.2.0 h767d61c_2 conda-forge
liblapack 3.9.0 31_h7ac8fdf_openblas conda-forge
liblapacke 3.9.0 31_he2f377e_openblas conda-forge
libnghttp2 1.51.0 hdcd2b5c_0 conda-forge
libopenblas 0.3.29 pthreads_h94d23a6_0 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libprotobuf 3.19.6 h3eb15da_0 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx 14.2.0 h8f9b012_2 conda-forge
libstdcxx-ng 14.2.0 h4852527_2 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
lzo 2.10 hd590300_1001 conda-forge
markdown 3.8 pyhd8ed1ab_0 conda-forge
markupsafe 3.0.2 py39h9399b63_1 conda-forge
multidict 6.4.3 py39h9399b63_0 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.2.1 pyhd8ed1ab_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
numexpr 2.10.2 py39h0a7e20a_100 conda-forge
numpy 1.24.3 py39h6183b62_0 conda-forge
oauthlib 3.2.2 pyhd8ed1ab_1 conda-forge
openssl 1.1.1w hd590300_0 conda-forge
opt_einsum 3.4.0 pyhd8ed1ab_1 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
parallel 20191122 0 conda-forge
pbzip2 1.1.13 h1fcc475_2 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pigz 2.8 h2797004_0 conda-forge
pip 25.1.1 pyh8b19718_0 conda-forge
propcache 0.3.1 py39h9399b63_0 conda-forge
protobuf 3.19.6 py39h227be39_0 conda-forge
pulp 2.8.0 py39hf3d152e_0 conda-forge
py-cpuinfo 9.0.0 pyhd8ed1ab_1 conda-forge
pyasn1 0.6.1 pyhd8ed1ab_2 conda-forge
pyasn1-modules 0.4.2 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pyfaidx 0.8.1.4 pyhdfd78af_0 bioconda
pyjwt 2.10.1 pyhd8ed1ab_0 conda-forge
pyopenssl 23.2.0 pyhd8ed1ab_1 conda-forge
pyparsing 3.2.3 pyhd8ed1ab_1 conda-forge
pypy3.6 7.3.2 h45e8706_2 conda-forge
pysam 0.21.0 py39h9abd093_0 bioconda
pysocks 1.7.1 pyha55dd90_7 conda-forge
pytables 3.8.0 py39hac3db9e_1 conda-forge
python 3.9.0 h2a148a8_4_cpython conda-forge
python-flatbuffers 25.2.10 pyhbc23db3_0 conda-forge
python-isal 1.7.2 py39h8cd3c5a_0 conda-forge
python-zlib-ng 0.4.3 py39h520f041_0 conda-forge
python_abi 3.9 7_cp39 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_1 conda-forge
pyvcf3 1.0.3 pyhdfd78af_0 bioconda
re2 2022.02.01 h9c3ff4c_0 conda-forge
readline 8.2 h8c095d6_2 conda-forge
requests 2.32.3 pyhd8ed1ab_1 conda-forge
requests-oauthlib 2.0.0 pyhd8ed1ab_1 conda-forge
rsa 4.9.1 pyhd8ed1ab_0 conda-forge
samtools 1.15.1 h6899075_1 bioconda
scipy 1.13.1 py39haf93ffa_0 conda-forge
setuptools 80.1.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhd8ed1ab_0 conda-forge
snappy 1.1.10 hdb0a2a9_1 conda-forge
sqlite 3.46.0 h6d4b2fc_0 conda-forge
tensorboard 2.8.0 pyhd8ed1ab_1 conda-forge
tensorboard-data-server 0.6.1 py39hd97740a_4 conda-forge
tensorboard-plugin-wit 1.8.1 pyhd8ed1ab_0 conda-forge
tensorflow 2.8.0 cpu_py39h4655687_0 conda-forge
tensorflow-addons 0.23.0 pypi_0 pypi
tensorflow-base 2.8.0 cpu_py39h7e02d9e_0 conda-forge
tensorflow-cpu 2.8.0 cpu_py39h718b53a_0 conda-forge
tensorflow-estimator 2.8.0 cpu_py39heaff504_0 conda-forge
termcolor 3.1.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
typing-extensions 4.13.2 h0e9735f_0 conda-forge
typing_extensions 4.13.2 pyh29332c3_0 conda-forge
tzdata 2025b h78e105d_0 conda-forge
urllib3 2.4.0 pyhd8ed1ab_0 conda-forge
werkzeug 3.1.3 pyhd8ed1ab_1 conda-forge
whatshap 1.7 py39h1f90b4d_1 bioconda
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
wrapt 1.17.2 py39h8cd3c5a_0 conda-forge
xopen 2.0.2 pyh707e725_2 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yarl 1.20.0 py39h9399b63_0 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zlib 1.2.13 h4ab18f5_6 conda-forge
zlib-ng 2.0.7 h0b41bf4_0 conda-forge
zstandard 0.23.0 py39h8cd3c5a_2 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
Code repository: https://github.com/HKU-BAL/Clair3
Basic information on how to use this tool:
- executable: run_clair3.sh
- help: -h, --help
- version: -v, --version
- description:
Additional information:
This container includes the following models in /clair3/models
hifi
hifi_revio
hifi_sequel2
ilmn
ont
ont_guppy2
ont_guppy5
r941_prom_hac_g238
r941_prom_hac_g360+g422
r941_prom_sup_g5014
Full documentation: https://github.com/HKU-BAL/Clair3
run_clair3.sh \
--bam_fn=${BAM} \
--ref_fn=${REF} \
--threads=${THREADS} \
--platform="ont" \ ## options: {ont,hifi,ilmn}
--model_path=${MODEL_PREFIX} \ ## absolute model path prefix
--output=${OUTPUT_DIR} ## absolute output path prefix
## pileup output file: ${OUTPUT_DIR}/pileup.vcf.gz
## full-alignment output file: ${OUTPUT_DIR}/full_alignment.vcf.gz
## Clair3 final output file: ${OUTPUT_DIR}/merge_output.vcf.gz