Main tool : artic
Full documentation: https://github.com/artic-network/fieldbioinformatics
Additional tools installed via micromamba:
List of packages in environment: "/opt/conda/envs/artic"
Name Version Build Channel
─────────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_python_abi3_support 1.0 hd8ed1ab_2 conda-forge
absl-py 2.3.1 pyhd8ed1ab_0 conda-forge
aiohappyeyeballs 2.6.1 pyhd8ed1ab_0 conda-forge
aiohttp 3.12.15 py310h3406613_0 conda-forge
aiosignal 1.4.0 pyhd8ed1ab_0 conda-forge
align_trim 1.0.1 pyhdfd78af_0 bioconda
amply 0.1.6 pyhd8ed1ab_1 conda-forge
annotated-types 0.7.0 pyhd8ed1ab_1 conda-forge
args 0.1.0 pyhd8ed1ab_1004 conda-forge
artic 1.8.0 pyhdfd78af_0 bioconda
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
bcftools 1.22 h3a4d415_1 bioconda
biopython 1.85 py310ha75aee5_1 conda-forge
blinker 1.9.0 pyhff2d567_0 conda-forge
blosc 1.21.5 h0f2a231_0 conda-forge
brotli-python 1.1.0 py310hf71b8c6_3 conda-forge
bwa 0.7.19 h577a1d6_1 bioconda
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
c-blosc2 2.15.2 h68e2383_0 conda-forge
ca-certificates 2025.8.3 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 2025.8.3 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py310h8deb56e_0 conda-forge
charset-normalizer 3.4.3 pyhd8ed1ab_0 conda-forge
clair3 1.2.0 py310h779eee5_0 bioconda
click 8.2.1 pyh707e725_0 conda-forge
clint 0.5.1 py_1 conda-forge
coin-or-cbc 2.10.12 h4d16d09_4 conda-forge
coin-or-cgl 0.60.9 hc46dffc_6 conda-forge
coin-or-clp 1.17.10 hc03379b_3 conda-forge
coin-or-osi 0.108.11 hf4fecb4_7 conda-forge
coin-or-utils 2.11.12 hc93afbd_6 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
coloredlogs 15.0.1 pyhd8ed1ab_4 conda-forge
colormath 3.0.0 pyhd8ed1ab_4 conda-forge
cpython 3.10.18 py310hd8ed1ab_0 conda-forge
cryptography 45.0.6 py310hed992bd_0 conda-forge
cyvcf2 0.31.0 py310h0ae5082_1 bioconda
docutils 0.22 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.3.0 pyhd8ed1ab_0 conda-forge
expat 2.7.1 hecca717_0 conda-forge
flatbuffers 23.5.26 h59595ed_1 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_3 conda-forge
fontconfig 2.15.0 h7e30c49_1 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.13.3 ha770c72_1 conda-forge
frozenlist 1.7.0 py310h9548a50_0 conda-forge
gast 0.6.0 pyhd8ed1ab_0 conda-forge
gawk 5.3.1 hcd3d067_0 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
google-auth 2.40.3 pyhd8ed1ab_0 conda-forge
google-auth-oauthlib 1.2.2 pyhd8ed1ab_0 conda-forge
google-pasta 0.2.0 pyhd8ed1ab_2 conda-forge
grpcio 1.59.3 py310h1b8f574_0 conda-forge
gsl 2.7 he838d99_0 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
h5py 3.13.0 nompi_py310h60e0fe6_100 conda-forge
hdf5 1.14.3 nompi_h2d575fe_109 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
htslib 1.22.1 h566b1c6_0 bioconda
humanfriendly 10.0 pyh707e725_8 conda-forge
humanize 4.13.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
importlib-metadata 8.7.0 pyhe01879c_1 conda-forge
iniconfig 2.0.0 pyhd8ed1ab_1 conda-forge
isa-l 2.31.1 hb9d3cd8_1 conda-forge
jinja2 3.1.6 pyhd8ed1ab_0 conda-forge
jsonschema 4.25.1 pyhe01879c_0 conda-forge
jsonschema-specifications 2025.4.1 pyh29332c3_0 conda-forge
k8 1.2 he8db53b_6 bioconda
kaleido-core 0.2.1 h3644ca4_0 conda-forge
keras 2.15.0 pyhd8ed1ab_0 conda-forge
kernel-headers_linux-64 5.14.0 he073ed8_2 conda-forge
keyutils 1.6.3 hb9d3cd8_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
lerc 4.0.0 h0aef613_1 conda-forge
libabseil 20230802.1 cxx17_h59595ed_0 conda-forge
libaec 1.1.4 h3f801dc_0 conda-forge
libasprintf 0.25.1 h3f43e3d_1 conda-forge
libblas 3.9.0 34_h59b9bed_openblas conda-forge
libcblas 3.9.0 34_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_4 conda-forge
libgcc-ng 15.1.0 h69a702a_4 conda-forge
libgettextpo 0.25.1 h3f43e3d_1 conda-forge
libgfortran 15.1.0 h69a702a_4 conda-forge
libgfortran5 15.1.0 hcea5267_4 conda-forge
libgomp 15.1.0 h767d61c_4 conda-forge
libgrpc 1.59.3 hd6c4280_0 conda-forge
libiconv 1.18 h3b78370_2 conda-forge
libjpeg-turbo 3.1.0 hb9d3cd8_0 conda-forge
liblapack 3.9.0 34_h7ac8fdf_openblas conda-forge
liblapacke 3.9.0 34_he2f377e_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_2 conda-forge
libpng 1.6.50 h421ea60_1 conda-forge
libprotobuf 4.24.4 hf27288f_0 conda-forge
libre2-11 2023.09.01 h7a70373_1 conda-forge
libsqlite 3.50.4 h0c1763c_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.1.0 h8f9b012_4 conda-forge
libstdcxx-ng 15.1.0 h4852527_4 conda-forge
libtiff 4.7.0 h8261f1e_6 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
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 h280c20c_1002 conda-forge
mafft 7.526 h4bc722e_0 conda-forge
markdown 3.8.2 pyhd8ed1ab_0 conda-forge
markdown-it-py 4.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 3.0.2 py310h89163eb_1 conda-forge
mathjax 2.7.7 ha770c72_3 conda-forge
mdurl 0.1.2 pyhd8ed1ab_1 conda-forge
minimap2 2.30 h577a1d6_0 bioconda
ml_dtypes 0.2.0 py310hcc13569_2 conda-forge
mpfr 4.2.1 h90cbb55_3 conda-forge
multidict 6.6.3 py310h89163eb_0 conda-forge
multiqc 1.30 pyhdfd78af_1 bioconda
narwhals 2.2.0 pyhcf101f3_0 conda-forge
natsort 8.4.0 pyh29332c3_1 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.4.2 pyh267e887_2 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
nspr 4.37 h29cc59b_0 conda-forge
nss 3.115 hc3c8bcf_0 conda-forge
numexpr 2.10.2 py310hdb6e06b_100 conda-forge
numpy 1.26.4 py310hb13e2d6_0 conda-forge
oauthlib 3.3.1 pyhd8ed1ab_0 conda-forge
openjpeg 2.5.3 h55fea9a_1 conda-forge
openssl 3.5.2 h26f9b46_0 conda-forge
opt_einsum 3.4.0 pyhd8ed1ab_1 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.3.2 py310h0158d43_0 conda-forge
parallel 20250622 ha770c72_0 conda-forge
pbzip2 1.1.13 h1fcc475_2 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pigz 2.8 hadc24fc_1 conda-forge
pillow 11.3.0 py310h7e6dc6c_0 conda-forge
pip 25.2 pyh8b19718_0 conda-forge
plotly 6.3.0 pyhd8ed1ab_0 conda-forge
pluggy 1.6.0 pyhd8ed1ab_0 conda-forge
polars-lts-cpu 1.32.3 py39h5734d0f_0 conda-forge
primalbedtools 0.10.1 pyhdfd78af_0 bioconda
propcache 0.3.1 py310h89163eb_0 conda-forge
protobuf 4.24.4 py310h620c231_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pulp 2.8.0 py310h9d216b0_2 conda-forge
py-cpuinfo 9.0.0 pyhd8ed1ab_1 conda-forge
pyaml-env 1.2.2 pyhd8ed1ab_0 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
pydantic 2.11.7 pyh3cfb1c2_0 conda-forge
pydantic-core 2.33.2 py310hbcd0ec0_0 conda-forge
pyfaidx 0.9.0.1 pyhdfd78af_0 bioconda
pygments 2.19.2 pyhd8ed1ab_0 conda-forge
pyjwt 2.10.1 pyhd8ed1ab_0 conda-forge
pyopenssl 25.1.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.2.3 pyhe01879c_2 conda-forge
pysam 0.23.3 py310h64e62c9_1 bioconda
pysocks 1.7.1 pyha55dd90_7 conda-forge
pytables 3.9.2 py310h73b55d5_3 conda-forge
pytest 8.4.1 pyhd8ed1ab_0 conda-forge
python 3.10.18 hd6af730_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-dotenv 1.1.1 pyhe01879c_0 conda-forge
python-flatbuffers 25.2.10 pyhbc23db3_0 conda-forge
python-gil 3.10.18 hd8ed1ab_0 conda-forge
python-isal 1.7.2 py310ha75aee5_0 conda-forge
python-kaleido 0.2.1 pyhd8ed1ab_0 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python-zlib-ng 0.5.1 py310h62b3d1f_0 conda-forge
python_abi 3.10 8_cp310 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_1 conda-forge
pyvcf3 1.0.4 py310h1fe012e_0 bioconda
pyyaml 6.0.2 py310h89163eb_2 conda-forge
re2 2023.09.01 h7f4b329_1 conda-forge
readline 8.2 h8c095d6_2 conda-forge
referencing 0.36.2 pyh29332c3_0 conda-forge
regex 2025.7.34 py310h7c4b9e2_0 conda-forge
requests 2.32.5 pyhd8ed1ab_0 conda-forge
requests-oauthlib 2.0.0 pyhd8ed1ab_1 conda-forge
rich 14.1.0 pyhe01879c_0 conda-forge
rich-click 1.8.9 pyhd8ed1ab_0 conda-forge
rpds-py 0.27.0 py310hd8f68c5_0 conda-forge
rsa 4.9.1 pyhd8ed1ab_0 conda-forge
samtools 1.22.1 h96c455f_0 bioconda
scipy 1.15.2 py310h1d65ade_0 conda-forge
seqtk 1.5 h577a1d6_1 bioconda
setuptools 80.9.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
snappy 1.1.10 hdb0a2a9_1 conda-forge
spectra 0.0.11 pyhd8ed1ab_2 conda-forge
sqlite 3.50.4 hbc0de68_0 conda-forge
sysroot_linux-64 2.34 h087de78_2 conda-forge
tensorboard 2.15.2 pyhd8ed1ab_0 conda-forge
tensorboard-data-server 0.7.0 py310h6c63255_2 conda-forge
tensorflow 2.15.0 cpu_py310h7825f03_2 conda-forge
tensorflow-base 2.15.0 cpu_py310h7e4d085_2 conda-forge
tensorflow-estimator 2.15.0 cpu_py310haacee6a_2 conda-forge
termcolor 3.1.0 pyhd8ed1ab_0 conda-forge
tiktoken 0.9.0 py310h6e8e937_0 conda-forge
tk 8.6.13 noxft_hd72426e_102 conda-forge
tomli 2.2.1 pyhe01879c_2 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
typeguard 4.4.4 pyhd8ed1ab_0 conda-forge
typing-extensions 4.15.0 h396c80c_0 conda-forge
typing-inspection 0.4.1 pyhd8ed1ab_0 conda-forge
typing_extensions 4.15.0 pyhcf101f3_0 conda-forge
tzdata 2025b h78e105d_0 conda-forge
urllib3 2.5.0 pyhd8ed1ab_0 conda-forge
werkzeug 3.1.3 pyhd8ed1ab_1 conda-forge
whatshap 2.8 py310h184ae93_0 bioconda
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
wrapt 1.14.1 py310h5764c6d_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 h280c20c_3 conda-forge
yarl 1.20.1 py310h89163eb_0 conda-forge
zipp 3.23.0 pyhd8ed1ab_0 conda-forge
zlib-ng 2.2.5 hde8ca8f_0 conda-forge
zstandard 0.23.0 py310h7c4b9e2_3 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge
There is also a very useful SOP: https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html And additional documentation: https://artic.readthedocs.io/en/latest/
A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore.
WARNING : This container does not contain the primer schemes found at https://github.com/artic-network/primer-schemes. Those will have to be downloaded and mounted separately. There are now commands to download the use the primers at runtime.
This image DOES contain the models downloaded with artic_get_models
# filtering reads
artic guppyplex --min-length 400 --max-length 700 --directory . --prefix SRR22452250_1.fastq.gz --output SRR22452250_1_filtered.fastq
# downloading medaka models for clair3
artic_get_models
# running the artic minion workflow
# the result files will all start with test*
artic minion --normalise 200 --medaka-model ont --threads 4 --read-file sample.fastq --scheme-directory primer-schemes --scheme-version 5.3.2 nCoV-2019 test
# running the artic minion workflow with user-provided primer bedfiles and references
artic minion --normalise 200 --threads 4 --model ont --read-file sample.fastq --scheme-name sars-cov-2 --scheme-version V5.3.2 name
In general, any primer scheme can be used as long as it meets artic's requirements.
Artic uses Clair3, which uses its own models for polishing. ONT chemistries update frequently, and artic can throw errors when corresponding ONT models are not found.
These are the models in this image:
# included models at /opt/conda/envs/artic/bin/models
hifi
hifi_revio
hifi_sequel2
ilmn
ont
ont_guppy5
r1041_e82_260bps_fast_g632
r1041_e82_260bps_hac_g632
r1041_e82_260bps_hac_v400
r1041_e82_260bps_hac_v410
r1041_e82_260bps_sup_g632
r1041_e82_260bps_sup_v400
r1041_e82_260bps_sup_v410
r1041_e82_400bps_fast_g632
r1041_e82_400bps_hac_g615
r1041_e82_400bps_hac_g632
r1041_e82_400bps_hac_v400
r1041_e82_400bps_hac_v410
r1041_e82_400bps_hac_v420
r1041_e82_400bps_hac_v430
r1041_e82_400bps_hac_v500
r1041_e82_400bps_hac_v520
r1041_e82_400bps_sup_g615
r1041_e82_400bps_sup_v400
r1041_e82_400bps_sup_v410
r1041_e82_400bps_sup_v420
r1041_e82_400bps_sup_v430
r1041_e82_400bps_sup_v500
r1041_e82_400bps_sup_v520
r104_e81_hac_g5015
r104_e81_sup_g5015
r941_prom_hac_g360+g422
r941_prom_sup_g5014