Main tool: verkko
Code repository: https://github.com/marbl/verkko
Basic information on how to use this tool:
- executable: verkko
- help: --help
- version: --version
- description: Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi or Oxford Nanopore Duplex and Oxford Nanopore simplex reads.
Full documentation: https://github.com/marbl/verkko
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
attrs 25.1.0 pyh71513ae_0 conda-forge
bamtools 2.5.2 hdcf5f25_5 bioconda
biopython 1.85 py39h8cd3c5a_1 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
ca-certificates 2025.1.31 hbcca054_0 conda-forge
certifi 2025.1.31 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py39h15c3d72_0 conda-forge
charset-normalizer 3.4.1 pyhd8ed1ab_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 1_metapackage conda-forge
configargparse 1.7 pyhd8ed1ab_1 conda-forge
connection_pool 0.0.3 pyhd3deb0d_0 conda-forge
datrie 0.8.2 py39h8cd3c5a_8 conda-forge
docutils 0.21.2 pyhd8ed1ab_1 conda-forge
dpath 2.2.0 pyha770c72_0 conda-forge
findutils 4.6.0 h166bdaf_1001 conda-forge
gettext 0.23.1 h5888daf_0 conda-forge
gettext-tools 0.23.1 h5888daf_0 conda-forge
gitdb 4.0.12 pyhd8ed1ab_0 conda-forge
gitpython 3.1.44 pyhff2d567_0 conda-forge
graphaligner 1.0.20 h06902ac_0 bioconda
gsl 2.7 he838d99_0 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
htslib 1.21 h5efdd21_0 bioconda
humanfriendly 10.0 pyh707e725_8 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
importlib_resources 6.5.2 pyhd8ed1ab_0 conda-forge
jemalloc 5.2.0 he1b5a44_0 conda-forge
jinja2 3.1.5 pyhd8ed1ab_0 conda-forge
jsonschema 4.23.0 pyhd8ed1ab_1 conda-forge
jsonschema-specifications 2024.10.1 pyhd8ed1ab_1 conda-forge
jupyter_core 5.7.2 pyh31011fe_1 conda-forge
k8 0.2.5 hdcf5f25_4 bioconda
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
libasprintf 0.23.1 h8e693c7_0 conda-forge
libasprintf-devel 0.23.1 h8e693c7_0 conda-forge
libblas 3.9.0 31_h59b9bed_openblas conda-forge
libcblas 3.9.0 31_he106b2a_openblas conda-forge
libcurl 8.8.0 hca28451_1 conda-forge
libdeflate 1.23 h4ddbbb0_0 conda-forge
libdivsufsort 2.0.2 h7b50bb2_10 bioconda
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libffi 3.4.6 h2dba641_0 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
libgettextpo-devel 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
liblzma-devel 5.6.4 hb9d3cd8_0 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.29 pthreads_h94d23a6_0 conda-forge
libprotobuf 3.14.0 h780b84a_0 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx 14.2.0 h8f9b012_2 conda-forge
libstdcxx-ng 14.2.0 h4852527_2 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.2.13 h4ab18f5_6 conda-forge
markupsafe 3.0.2 py39h9399b63_1 conda-forge
mashmap 3.1.3 h07ea13f_1 bioconda
meryl 1.4.1 h9948957_2 bioconda
minimap2 2.28 he4a0461_3 bioconda
nbformat 5.10.4 pyhd8ed1ab_1 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.2.1 pyhd8ed1ab_0 conda-forge
numpy 2.0.2 py39h9cb892a_1 conda-forge
openblas 0.3.29 pthreads_h6ec200e_0 conda-forge
openssl 3.4.1 h7b32b05_0 conda-forge
packaging 24.2 pyhd8ed1ab_2 conda-forge
parasail-python 1.3.4 py39heaaa4ec_2 bioconda
perl 5.32.1 7_hd590300_perl5 conda-forge
pip 25.0.1 pyh8b19718_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_2 conda-forge
plac 1.4.3 pyhd8ed1ab_1 conda-forge
platformdirs 4.3.6 pyhd8ed1ab_1 conda-forge
protobuf 3.14.0 py39he80948d_1 conda-forge
psutil 6.1.1 py39h8cd3c5a_0 conda-forge
pulp 2.7.0 py39hf3d152e_1 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pyparsing 3.2.1 pyhd8ed1ab_0 conda-forge
pysam 0.22.1 py39h61809e1_2 bioconda
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.9.19 h0755675_0_cpython conda-forge
python-fastjsonschema 2.21.1 pyhd8ed1ab_0 conda-forge
python_abi 3.9 5_cp39 conda-forge
pyyaml 6.0.2 py39h9399b63_2 conda-forge
readline 8.2 h8c095d6_2 conda-forge
referencing 0.36.2 pyh29332c3_0 conda-forge
requests 2.32.3 pyhd8ed1ab_1 conda-forge
reretry 0.11.8 pyhd8ed1ab_1 conda-forge
rpds-py 0.23.1 py39h3506688_0 conda-forge
samtools 1.21 h50ea8bc_0 bioconda
seqtk 1.4 he4a0461_2 bioconda
setuptools 75.8.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhd8ed1ab_0 conda-forge
smart_open 7.1.0 pyhd8ed1ab_0 conda-forge
smmap 5.0.2 pyhd8ed1ab_0 conda-forge
snakemake-minimal 7.32.4 pyhdfd78af_1 bioconda
stopit 1.1.2 pyhd8ed1ab_1 conda-forge
tabulate 0.9.0 pyhd8ed1ab_2 conda-forge
throttler 1.2.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toposort 1.10 pyhd8ed1ab_1 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
typing_extensions 4.12.2 pyha770c72_1 conda-forge
tzdata 2025a h78e105d_0 conda-forge
urllib3 2.3.0 pyhd8ed1ab_0 conda-forge
verkko 2.2.1 h45dadce_0 bioconda
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
winnowmap 2.03 h43eeafb_2 bioconda
wrapt 1.17.2 py39h8cd3c5a_0 conda-forge
xz 5.6.4 hbcc6ac9_0 conda-forge
xz-gpl-tools 5.6.4 hbcc6ac9_0 conda-forge
xz-tools 5.6.4 hb9d3cd8_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yte 1.5.7 pyha770c72_0 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zlib 1.2.13 h4ab18f5_6 conda-forge
zstandard 0.23.0 py39h08a7858_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forgeverkko -d <work-directory> --hifi <hifi-read-files> [--nano <ont-read-files>]