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
───────────────────────────────────────────────────────────────────────────────────────────
_openmp_mutex 4.5 7_kmp_llvm conda-forge
_python_abi3_support 1.0 hd8ed1ab_2 conda-forge
align_trim 1.1.0 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 1.10.0 pyhdfd78af_0 bioconda
attrs 26.1.0 pyhcf101f3_0 conda-forge
aws-c-auth 0.10.1 h2d2dd48_2 conda-forge
aws-c-cal 0.9.13 h2c9d079_1 conda-forge
aws-c-common 0.12.6 hb03c661_0 conda-forge
aws-c-compression 0.3.2 h8b1a151_0 conda-forge
aws-c-http 0.10.12 h4bacb7b_1 conda-forge
aws-c-io 0.26.3 hc87160b_0 conda-forge
aws-c-s3 0.11.5 h6d69fc9_5 conda-forge
aws-c-sdkutils 0.2.4 h8b1a151_4 conda-forge
aws-checksums 0.2.10 h8b1a151_0 conda-forge
backports.zstd 1.3.0 py311h6b1f9c4_0 conda-forge
bcftools 1.23.1 hb2cee57_0 bioconda
biopython 1.87 py311h49ec1c0_0 conda-forge
blosc 1.21.6 he440d0b_1 conda-forge
brotli-python 1.2.0 py311h66f275b_1 conda-forge
bwa 0.7.19 h577a1d6_1 bioconda
bzip2 1.0.8 hda65f42_9 conda-forge
c-ares 1.34.6 hb03c661_0 conda-forge
c-blosc2 2.23.1 hc31b594_0 conda-forge
ca-certificates 2026.2.25 hbd8a1cb_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
certifi 2026.2.25 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py311hf29c0ef_0 conda-forge
charset-normalizer 3.4.7 pyhd8ed1ab_0 conda-forge
clair3 2.0.0 py311hbc58adc_2 bioconda
click 8.3.2 pyhc90fa1f_0 conda-forge
clint 0.5.1 py_1 conda-forge
coin-or-cbc 2.10.13 h4d16d09_0 conda-forge
coin-or-cgl 0.60.10 hc46dffc_0 conda-forge
coin-or-clp 1.17.11 hc03379b_0 conda-forge
coin-or-osi 0.108.12 hf4fecb4_0 conda-forge
coin-or-utils 2.11.13 hc93afbd_0 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 3.11.15 py311hd8ed1ab_0 conda-forge
cyvcf2 0.31.1 py311h96fc995_3 bioconda
docutils 0.22.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.3.1 pyhd8ed1ab_0 conda-forge
expat 2.7.5 hecca717_0 conda-forge
filelock 3.29.0 pyhd8ed1ab_0 conda-forge
fmt 12.1.0 hff5e90c_0 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 2.17.1 h27c8c51_0 conda-forge
fonts-conda-forge 1 hc364b38_1 conda-forge
fsspec 2026.3.0 pyhd8ed1ab_0 conda-forge
gawk 5.3.1 hcd3d067_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
gmpy2 2.3.0 py311h92a432a_1 conda-forge
gsl 2.7 he838d99_0 conda-forge
h2 4.3.0 pyhcf101f3_0 conda-forge
h5py 3.16.0 nompi_py311hfef529e_102 conda-forge
hdf5 2.1.0 nompi_hd4fcb43_104 conda-forge
hdf5plugin 6.0.0 py311h41e6a36_5 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
htslib 1.23.1 h633afcb_0 bioconda
humanfriendly 10.0 pyh707e725_8 conda-forge
humanize 4.15.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 78.3 h33c6efd_0 conda-forge
idna 3.11 pyhd8ed1ab_0 conda-forge
importlib-metadata 8.8.0 pyhcf101f3_0 conda-forge
iniconfig 2.3.0 pyhd8ed1ab_0 conda-forge
isa-l 2.31.1 hb9d3cd8_1 conda-forge
jinja2 3.1.6 pyhcf101f3_1 conda-forge
jsonschema 4.26.0 pyhcf101f3_0 conda-forge
jsonschema-specifications 2025.9.1 pyhcf101f3_0 conda-forge
k8 1.2 he8db53b_6 bioconda
kaleido-core 0.2.1 h3644ca4_0 conda-forge
kernel-headers_linux-64 6.12.0 he073ed8_6 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
krb5 1.22.2 ha1258a1_0 conda-forge
lcms2 2.18 h0c24ade_0 conda-forge
ld_impl_linux-64 2.45.1 default_hbd61a6d_102 conda-forge
lerc 4.1.0 hdb68285_0 conda-forge
libabseil 20260107.1 cxx17_h7b12aa8_0 conda-forge
libaec 1.1.5 h088129d_0 conda-forge
libasprintf 0.25.1 h3f43e3d_1 conda-forge
libblas 3.11.0 6_h4a7cf45_openblas conda-forge
libcblas 3.11.0 6_h0358290_openblas conda-forge
libcurl 8.19.0 hcf29cc6_0 conda-forge
libdeflate 1.25 h17f619e_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.5 hecca717_0 conda-forge
libffi 3.5.2 h3435931_0 conda-forge
libfreetype 2.14.3 ha770c72_0 conda-forge
libfreetype6 2.14.3 h73754d4_0 conda-forge
libgcc 15.2.0 he0feb66_18 conda-forge
libgcc-ng 15.2.0 h69a702a_18 conda-forge
libgettextpo 0.25.1 h3f43e3d_1 conda-forge
libgfortran 15.2.0 h69a702a_18 conda-forge
libgfortran5 15.2.0 h68bc16d_18 conda-forge
libiconv 1.18 h3b78370_2 conda-forge
libjpeg-turbo 3.1.4.1 hb03c661_0 conda-forge
liblapack 3.11.0 6_h47877c9_openblas conda-forge
liblapacke 3.11.0 6_h6ae95b6_openblas conda-forge
liblzma 5.8.3 hb03c661_0 conda-forge
libnghttp2 1.68.1 h877daf1_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.32 openmp_hd680484_0 conda-forge
libpng 1.6.58 h421ea60_0 conda-forge
libprotobuf 6.33.5 h2b00c02_0 conda-forge
libsqlite 3.53.0 hf4e2dac_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.2.0 h934c35e_18 conda-forge
libstdcxx-ng 15.2.0 hdf11a46_18 conda-forge
libtiff 4.7.1 h9d88235_1 conda-forge
libtorch 2.10.0 cpu_generic_hd32bbb9_3 conda-forge
libuuid 2.42 h5347b49_0 conda-forge
libuv 1.51.0 hb03c661_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
libzlib 1.3.2 h25fd6f3_2 conda-forge
lightning-utilities 0.15.3 pyhd8ed1ab_0 conda-forge
llvm-openmp 22.1.3 h4922eb0_0 conda-forge
longphase 2.0.1 h4e109e1_1 bioconda
lz4-c 1.10.0 h5888daf_1 conda-forge
mafft 7.526 h4bc722e_0 conda-forge
markdown 3.10.2 pyhcf101f3_0 conda-forge
markdown-it-py 4.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 3.0.3 py311h3778330_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
mpc 1.4.0 he0a73b1_0 conda-forge
mpfr 4.2.2 he0a73b1_0 conda-forge
mpmath 1.3.0 pyhd8ed1ab_1 conda-forge
multiqc 1.33 pyhdfd78af_0 bioconda
narwhals 2.20.0 pyhcf101f3_0 conda-forge
natsort 8.4.0 pyhcf101f3_2 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.6.1 pyhcf101f3_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
nspr 4.38 h29cc59b_0 conda-forge
nss 3.118 h445c969_0 conda-forge
numexpr 2.14.1 py311h3143de2_101 conda-forge
numpy 2.4.3 py311h2e04523_0 conda-forge
openjpeg 2.5.4 h55fea9a_0 conda-forge
openssl 3.6.2 h35e630c_0 conda-forge
optree 0.19.0 py311hdf67eae_0 conda-forge
packaging 26.1 pyhc364b38_0 conda-forge
pandas 3.0.2 py311h8032f78_0 conda-forge
parallel 20260122 ha770c72_0 conda-forge
pbzip2 1.1.13 h1fcc475_2 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pigz 2.8 h421ea60_2 conda-forge
pillow 12.2.0 py311hf88fc01_0 conda-forge
pip 26.0.1 pyh8b19718_0 conda-forge
plotly 6.6.0 pyhd8ed1ab_0 conda-forge
pluggy 1.6.0 pyhf9edf01_1 conda-forge
polars 1.40.0 pyh58ad624_0 conda-forge
polars-lts-cpu 1.34.0.deprecated hc364b38_0 conda-forge
polars-runtime-32 1.40.0 py310hffdcd12_0 conda-forge
polars-runtime-compat 1.40.0 py310hbcd5346_0 conda-forge
primalbedtools 1.0.0 pyhdfd78af_0 bioconda
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pulp 2.8.0 py311h77a8cca_3 conda-forge
pyaml-env 1.2.2 pyhd8ed1ab_0 conda-forge
pybind11 3.0.1 pyh7a1b43c_0 conda-forge
pybind11-abi 11 hc364b38_1 conda-forge
pybind11-global 3.0.1 pyhc7ab6ef_0 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pydantic 2.13.3 pyhcf101f3_0 conda-forge
pydantic-core 2.46.3 py311h902ca64_0 conda-forge
pyfaidx 0.9.0.4 pyhdfd78af_0 bioconda
pygments 2.20.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.3.2 pyhcf101f3_0 conda-forge
pysam 0.23.3 py311haeb7863_2 bioconda
pysocks 1.7.1 pyha55dd90_7 conda-forge
pytest 9.0.3 pyhc364b38_1 conda-forge
python 3.11.15 hd63d673_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-dotenv 1.2.2 pyhcf101f3_0 conda-forge
python-gil 3.11.15 hd8ed1ab_0 conda-forge
python-isal 1.8.0 py311h49ec1c0_1 conda-forge
python-kaleido 0.2.1 pyhd8ed1ab_0 conda-forge
python-zlib-ng 1.0.0 py311h15805fc_1 conda-forge
python_abi 3.11 8_cp311 conda-forge
pytorch 2.10.0 cpu_generic_py311_hf96630c_3 conda-forge
pytorch-cpu 2.10.0 cpu_generic_h6ea6555_3 conda-forge
pyvcf3 1.0.4 py311haab0aaa_0 bioconda
pyyaml 6.0.3 py311h3778330_1 conda-forge
readline 8.3 h853b02a_0 conda-forge
referencing 0.37.0 pyhcf101f3_0 conda-forge
regex 2026.4.4 py311h49ec1c0_0 conda-forge
requests 2.33.1 pyhcf101f3_0 conda-forge
rich 15.0.0 pyhcf101f3_0 conda-forge
rich-click 1.9.7 pyh8f84b5b_0 conda-forge
rpds-py 0.30.0 py311h902ca64_0 conda-forge
s2n 1.7.1 h1cbb8d7_1 conda-forge
samtools 1.23.1 ha83d96e_0 bioconda
scipy 1.17.1 py311hbe70eeb_0 conda-forge
seqtk 1.5 h577a1d6_1 bioconda
setuptools 82.0.1 pyh332efcf_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
sleef 3.9.0 ha0421bc_0 conda-forge
snappy 1.2.2 h03e3b7b_1 conda-forge
spectra 0.0.11 pyhd8ed1ab_2 conda-forge
sqlite 3.53.0 h04a0ce9_0 conda-forge
sympy 1.14.0 pyh2585a3b_106 conda-forge
sysroot_linux-64 2.39 hc4b9eeb_6 conda-forge
tiktoken 0.12.0 py311h9a14573_3 conda-forge
tk 8.6.13 noxft_h366c992_103 conda-forge
tomli 2.4.1 pyhcf101f3_0 conda-forge
torchmetrics 1.9.0 pyhd8ed1ab_0 conda-forge
tqdm 4.67.3 pyh8f84b5b_0 conda-forge
typeguard 4.5.1 pyhd8ed1ab_0 conda-forge
typing-extensions 4.15.0 h396c80c_0 conda-forge
typing-inspection 0.4.2 pyhd8ed1ab_1 conda-forge
typing_extensions 4.15.0 pyhcf101f3_0 conda-forge
tzdata 2025c hc9c84f9_1 conda-forge
urllib3 2.6.3 pyhd8ed1ab_0 conda-forge
whatshap 2.8 py311he264feb_0 bioconda
wheel 0.46.3 pyhd8ed1ab_0 conda-forge
xopen 2.0.2 pyh707e725_2 conda-forge
xorg-libxau 1.0.12 hb03c661_1 conda-forge
xorg-libxdmcp 1.1.5 hb03c661_1 conda-forge
yaml 0.2.5 h280c20c_3 conda-forge
zipp 3.23.1 pyhcf101f3_0 conda-forge
zlib-ng 2.3.3 hceb46e0_1 conda-forge
zstandard 0.25.0 py311haee01d2_1 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forge
There is also a very useful SOP: https://artic.network/fieldbioinformatics/fieldbioinformatics-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
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_g615
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