Main tool : artic
Full documentation: https://github.com/artic-network/fieldbioinformatics
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 2.1.0 pyhd8ed1ab_1 conda-forge
aiohappyeyeballs 2.6.1 pyhd8ed1ab_0 conda-forge
aiohttp 3.11.14 py39h9399b63_0 conda-forge
aiosignal 1.3.2 pyhd8ed1ab_0 conda-forge
amply 0.1.6 pyhd8ed1ab_1 conda-forge
args 0.1.0 pyhd8ed1ab_1004 conda-forge
artic 1.6.2 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 1.17 h3cc50cf_1 bioconda
biopython 1.85 py39h8cd3c5a_1 conda-forge
blinker 1.9.0 pyhff2d567_0 conda-forge
blosc 1.21.5 h0f2a231_0 conda-forge
brotli 1.1.0 hb9d3cd8_2 conda-forge
brotli-bin 1.1.0 hb9d3cd8_2 conda-forge
brotli-python 1.1.0 py39hf88036b_2 conda-forge
bwa 0.7.18 he4a0461_1 bioconda
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.4 hb9d3cd8_0 conda-forge
c-blosc2 2.12.0 hb4ffafa_0 conda-forge
ca-certificates 2025.1.31 hbcca054_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 3.4.1 pyhd8ed1ab_0 conda-forge
clair3 1.0.10 py39hd649744_1 bioconda
click 8.1.8 pyh707e725_0 conda-forge
clint 0.5.1 py_1 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
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
coloredlogs 15.0.1 pyhd8ed1ab_4 conda-forge
colormath 3.0.0 pyhd8ed1ab_4 conda-forge
contourpy 1.3.0 py39h74842e3_2 conda-forge
cryptography 39.0.0 py39hd598818_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
cyvcf2 0.30.16 py39h3ba1b09_1 bioconda
docutils 0.21.2 pyhd8ed1ab_1 conda-forge
exceptiongroup 1.2.2 pyhd8ed1ab_1 conda-forge
expat 2.6.4 h5888daf_0 conda-forge
fonttools 4.56.0 py39h9399b63_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
frozenlist 1.5.0 py39h9399b63_1 conda-forge
future 1.0.0 pyhd8ed1ab_2 conda-forge
gast 0.6.0 pyhd8ed1ab_0 conda-forge
gawk 5.3.1 hcd3d067_0 conda-forge
gdbm 1.18 h0a1914f_2 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
google-auth 2.38.0 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
gsl 2.7 he838d99_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
humanfriendly 10.0 pyh707e725_8 conda-forge
humanize 4.12.1 pyhd8ed1ab_0 conda-forge
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
importlib-resources 6.5.2 pyhd8ed1ab_0 conda-forge
importlib_resources 6.5.2 pyhd8ed1ab_0 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
jpeg 9e h0b41bf4_3 conda-forge
k8 0.2.5 hdcf5f25_4 bioconda
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
kiwisolver 1.4.7 py39h74842e3_0 conda-forge
krb5 1.20.1 hf9c8cef_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libasprintf 0.23.1 h8e693c7_0 conda-forge
libblas 3.9.0 31_h59b9bed_openblas conda-forge
libbrotlicommon 1.1.0 hb9d3cd8_2 conda-forge
libbrotlidec 1.1.0 hb9d3cd8_2 conda-forge
libbrotlienc 1.1.0 hb9d3cd8_2 conda-forge
libcblas 3.9.0 31_he106b2a_openblas conda-forge
libcurl 7.87.0 h6312ad2_0 conda-forge
libdeflate 1.23 h4ddbbb0_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.6.4 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
libgettextpo 0.23.1 h5888daf_0 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
liblzma 5.6.4 hb9d3cd8_0 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
libtiff 4.2.0 hf544144_3 conda-forge
libwebp-base 1.5.0 h851e524_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
lzo 2.10 hd590300_1001 conda-forge
lzstring 1.0.4 pyhd8ed1ab_1003 conda-forge
mafft 7.526 h4bc722e_0 conda-forge
markdown 3.6 pyhd8ed1ab_0 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_1 conda-forge
markupsafe 3.0.2 py39h9399b63_1 conda-forge
matplotlib-base 3.9.4 py39h16632d1_0 conda-forge
mdurl 0.1.2 pyhd8ed1ab_1 conda-forge
minimap2 2.28 he4a0461_3 bioconda
mpfr 4.2.1 h90cbb55_3 conda-forge
multidict 6.2.0 py39h9399b63_0 conda-forge
multiqc 1.19 pyhdfd78af_0 bioconda
munkres 1.1.4 pyh9f0ad1d_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 1.26.4 py39h474f0d3_0 conda-forge
oauthlib 3.2.2 pyhd8ed1ab_1 conda-forge
olefile 0.47 pyhd8ed1ab_1 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openssl 1.1.1w hd590300_0 conda-forge
opt_einsum 3.4.0 pyhd8ed1ab_1 conda-forge
packaging 24.2 pyhd8ed1ab_2 conda-forge
pandas 2.2.3 py39h3b40f6f_2 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
pillow 8.2.0 py39hf95b381_1 conda-forge
pip 25.0.1 pyh8b19718_0 conda-forge
pluggy 1.5.0 pyhd8ed1ab_1 conda-forge
propcache 0.2.1 py39h9399b63_1 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
pyaml-env 1.2.2 pyhd8ed1ab_0 conda-forge
pyasn1 0.6.1 pyhd8ed1ab_2 conda-forge
pyasn1-modules 0.4.1 pyhd8ed1ab_1 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pyfaidx 0.8.1.3 pyhdfd78af_0 bioconda
pygments 2.19.1 pyhd8ed1ab_0 conda-forge
pyjwt 2.10.1 pyhd8ed1ab_0 conda-forge
pyopenssl 23.2.0 pyhd8ed1ab_1 conda-forge
pyparsing 3.2.1 pyhd8ed1ab_0 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
pytest 8.3.5 pyhd8ed1ab_0 conda-forge
python 3.9.0 h2a148a8_4_cpython conda-forge
python-dateutil 2.9.0.post0 pyhff2d567_1 conda-forge
python-flatbuffers 25.2.10 pyhbc23db3_0 conda-forge
python-isal 1.7.2 py39h8cd3c5a_0 conda-forge
python-tzdata 2025.1 pyhd8ed1ab_0 conda-forge
python-zlib-ng 0.4.3 py39h520f041_0 conda-forge
python_abi 3.9 5_cp39 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_1 conda-forge
pyvcf3 1.0.3 pyhdfd78af_0 bioconda
pyyaml 6.0.2 py39h9399b63_2 conda-forge
qhull 2020.2 h434a139_5 conda-forge
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
rich 13.9.4 pyhd8ed1ab_1 conda-forge
rich-click 1.8.8 pyhd8ed1ab_0 conda-forge
rsa 4.9 pyhd8ed1ab_1 conda-forge
samtools 1.15.1 h6899075_1 bioconda
scipy 1.13.1 py39haf93ffa_0 conda-forge
seqtk 1.4 he4a0461_2 bioconda
setuptools 75.8.2 pyhff2d567_0 conda-forge
simplejson 3.20.1 py39h8cd3c5a_0 conda-forge
six 1.17.0 pyhd8ed1ab_0 conda-forge
snappy 1.1.10 hdb0a2a9_1 conda-forge
spectra 0.0.11 pyhd8ed1ab_2 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-base 2.8.0 cpu_py39h7e02d9e_0 conda-forge
tensorflow-estimator 2.8.0 cpu_py39heaff504_0 conda-forge
termcolor 2.5.0 pyhd8ed1ab_1 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.2.1 pyhd8ed1ab_1 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
typing-extensions 4.12.2 hd8ed1ab_1 conda-forge
typing_extensions 4.12.2 pyha770c72_1 conda-forge
tzdata 2025a h78e105d_0 conda-forge
unicodedata2 16.0.0 py39h8cd3c5a_0 conda-forge
urllib3 2.3.0 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
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.18.3 py39h9399b63_1 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_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 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_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
r104_e81_hac_g5015
r104_e81_sup_g5015
r941_prom_hac_g360+g422
r941_prom_sup_g5014