Main tool: Virsorter 2
Code repository: https://github.com/jiarong/VirSorter2
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
amply 0.1.6 pyhd8ed1ab_1 conda-forge
appdirs 1.4.4 pyhd8ed1ab_1 conda-forge
arrow 1.3.0 pyhd8ed1ab_1 conda-forge
attrs 25.3.0 pyh71513ae_0 conda-forge
binaryornot 0.4.4 pyhd8ed1ab_2 conda-forge
boltons 24.0.0 pyhd8ed1ab_1 conda-forge
brotli-python 1.1.0 py310hf71b8c6_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.4.26 hbd8a1cb_0 conda-forge
certifi 2025.4.26 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py310h8deb56e_0 conda-forge
chardet 5.2.0 pyhd8ed1ab_3 conda-forge
charset-normalizer 3.4.2 pyhd8ed1ab_0 conda-forge
click 8.2.1 pyh707e725_0 conda-forge
coin-or-cbc 2.10.12 h00e76a6_2 conda-forge
coin-or-cgl 0.60.9 h82e2f02_4 conda-forge
coin-or-clp 1.17.10 h8a7a1e7_1 conda-forge
coin-or-osi 0.108.11 h96cc833_4 conda-forge
coin-or-utils 2.11.12 h3a12e53_2 conda-forge
coincbc 2.10.12 2_metapackage conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
conda 23.7.4 py310hff52083_0 conda-forge
conda-package-handling 1.9.0 py310h5764c6d_1 conda-forge
configargparse 1.7 pyhd8ed1ab_1 conda-forge
cookiecutter 2.6.0 pyhd8ed1ab_1 conda-forge
cryptography 45.0.2 py310h6c63255_0 conda-forge
datrie 0.8.2 py310ha75aee5_8 conda-forge
docutils 0.21.2 pyhd8ed1ab_1 conda-forge
fmt 10.2.1 h00ab1b0_0 conda-forge
git 2.49.0 pl5321hc2ff736_1 conda-forge
gitdb 4.0.12 pyhd8ed1ab_0 conda-forge
gitpython 3.1.44 pyhff2d567_0 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
importlib_resources 6.5.2 pyhd8ed1ab_0 conda-forge
jinja2 3.1.6 pyhd8ed1ab_0 conda-forge
jsonpatch 1.33 pyhd8ed1ab_1 conda-forge
jsonpointer 3.0.0 py310hff52083_1 conda-forge
jsonschema 4.23.0 pyhd8ed1ab_1 conda-forge
jsonschema-specifications 2025.4.1 pyh29332c3_0 conda-forge
jupyter_core 5.7.2 pyh31011fe_1 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
libarchive 3.7.7 h75ea233_4 conda-forge
libblas 3.9.0 31_h59b9bed_openblas conda-forge
libcblas 3.9.0 31_he106b2a_openblas conda-forge
libcurl 8.13.0 h332b0f4_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 3.4.6 h2dba641_1 conda-forge
libgcc 15.1.0 h767d61c_2 conda-forge
libgcc-ng 15.1.0 h69a702a_2 conda-forge
libgfortran 15.1.0 h69a702a_2 conda-forge
libgfortran5 15.1.0 hcea5267_2 conda-forge
libgomp 15.1.0 h767d61c_2 conda-forge
libiconv 1.18 h4ce23a2_1 conda-forge
liblapack 3.9.0 31_h7ac8fdf_openblas conda-forge
liblapacke 3.9.0 31_he2f377e_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_1 conda-forge
liblzma-devel 5.8.1 hb9d3cd8_1 conda-forge
libmamba 1.5.1 had39da4_2 conda-forge
libmambapy 1.5.1 py310h39ff949_2 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.29 pthreads_h94d23a6_0 conda-forge
libsolv 0.7.32 h7955e40_2 conda-forge
libsqlite 3.49.2 hee588c1_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.1.0 h8f9b012_2 conda-forge
libstdcxx-ng 15.1.0 h4852527_2 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.13.8 h4bc477f_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
lz4-c 1.10.0 h5888daf_1 conda-forge
lzo 2.10 hd590300_1001 conda-forge
mamba 1.5.1 py310h51d5547_2 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_1 conda-forge
markupsafe 3.0.2 py310h89163eb_1 conda-forge
mdurl 0.1.2 pyhd8ed1ab_1 conda-forge
nbformat 5.10.4 pyhd8ed1ab_1 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
openssl 3.5.0 h7b32b05_1 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pcre2 10.45 hc749103_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pip 25.1.1 pyh8b19718_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_2 conda-forge
platformdirs 4.3.8 pyhe01879c_0 conda-forge
pluggy 1.6.0 pyhd8ed1ab_0 conda-forge
psutil 7.0.0 py310ha75aee5_0 conda-forge
pulp 2.7.0 py310hff52083_1 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.6 py310ha75aee5_2 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pygments 2.19.1 pyhd8ed1ab_0 conda-forge
pyopenssl 25.1.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.2.3 pyhd8ed1ab_1 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.10.0 h543edf9_3_cpython conda-forge
python-dateutil 2.9.0.post0 pyhff2d567_1 conda-forge
python-fastjsonschema 2.21.1 pyhd8ed1ab_0 conda-forge
python-slugify 8.0.4 pyhd8ed1ab_1 conda-forge
python_abi 3.10 7_cp310 conda-forge
pyyaml 6.0.2 py310h89163eb_2 conda-forge
ratelimiter 1.2.0 pyhd8ed1ab_1003 conda-forge
readline 8.2 h8c095d6_2 conda-forge
referencing 0.36.2 pyh29332c3_0 conda-forge
reproc 14.2.5.post0 hb9d3cd8_0 conda-forge
reproc-cpp 14.2.5.post0 h5888daf_0 conda-forge
requests 2.32.3 pyhd8ed1ab_1 conda-forge
rich 14.0.0 pyh29332c3_0 conda-forge
rpds-py 0.25.1 py310hbcd0ec0_0 conda-forge
ruamel.yaml 0.16.12 py310h5764c6d_3 conda-forge
ruamel.yaml.clib 0.2.8 py310ha75aee5_1 conda-forge
setuptools 80.8.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhd8ed1ab_0 conda-forge
smmap 5.0.2 pyhd8ed1ab_0 conda-forge
snakemake-minimal 5.26.0 py_0 bioconda
sqlite 3.49.2 h9eae976_0 conda-forge
text-unidecode 1.3 pyhd8ed1ab_2 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toolz 1.0.0 pyhd8ed1ab_1 conda-forge
toposort 1.10 pyhd8ed1ab_1 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
types-python-dateutil 2.9.0.20250516 pyhd8ed1ab_0 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
virsorter 2.2.4 pyhdfd78af_2 bioconda
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
wrapt 1.17.2 py310ha75aee5_0 conda-forge
xz 5.8.1 hbcc6ac9_1 conda-forge
xz-gpl-tools 5.8.1 hbcc6ac9_1 conda-forge
xz-tools 5.8.1 hb9d3cd8_1 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yaml-cpp 0.8.0 h3f2d84a_0 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zstandard 0.23.0 py310ha75aee5_2 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forgeBasic information on how to use this tool:
- executable: virsorter
- help: --help
- version: --version
- description: |
VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.
Additional information:
Image does not contain virsorter's database, but it should be downloadable for the user with
virsorter setup -d /db -j 4or
wget -O db.tgz https://osf.io/v46sc/download
tar -xzf db.tgz --no-same-owner
rm db.tgz
virsorter config --init-source --db-dir=./dbFull documentation: https://github.com/jiarong/VirSorter2?tab=readme-ov-file SOP : https://www.protocols.io/view/viral-sequence-identification-sop-with-virsorter2-5qpvoyqebg4o/v3
virsorter run -w virsorter2.test.out -i test.fa -j 1