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
argparse-dataclass 2.0.0 pyhd8ed1ab_1 conda-forge
attrs 25.4.0 pyhcf101f3_1 conda-forge
backports.zstd 1.2.0 py311h6b1f9c4_0 conda-forge
bamtools 2.5.3 he132191_0 bioconda
biopython 1.86 py311h49ec1c0_0 conda-forge
brotli-python 1.2.0 py311h66f275b_1 conda-forge
bwa 0.7.19 h577a1d6_1 bioconda
bzip2 1.0.8 hda65f42_8 conda-forge
c-ares 1.34.6 hb03c661_0 conda-forge
ca-certificates 2025.11.12 hbd8a1cb_0 conda-forge
certifi 2025.11.12 pyhd8ed1ab_0 conda-forge
charset-normalizer 3.4.4 pyhd8ed1ab_0 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_8 conda-forge
coin-or-utils 2.11.12 hc93afbd_7 conda-forge
coincbc 2.10.12 4_metapackage conda-forge
configargparse 1.7.1 pyhe01879c_0 conda-forge
connection_pool 0.0.3 pyhd3deb0d_0 conda-forge
datrie 0.8.3 py311h49ec1c0_0 conda-forge
docutils 0.22.3 pyhd8ed1ab_0 conda-forge
dpath 2.2.0 pyha770c72_1 conda-forge
findutils 4.10.0 h86094a7_1 conda-forge
gitdb 4.0.12 pyhd8ed1ab_0 conda-forge
gitpython 3.1.45 pyhff2d567_0 conda-forge
graphaligner 1.0.20 h06902ac_1 bioconda
gsl 2.7 he838d99_0 conda-forge
h2 4.3.0 pyhcf101f3_0 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
htslib 1.22.1 h566b1c6_0 bioconda
humanfriendly 10.0 pyh707e725_8 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
idna 3.11 pyhd8ed1ab_0 conda-forge
jemalloc 5.2.0 he1b5a44_0 conda-forge
jinja2 3.1.6 pyhcf101f3_1 conda-forge
jsoncpp 1.9.6 hf42df4d_1 conda-forge
jsonschema 4.25.1 pyhe01879c_0 conda-forge
jsonschema-specifications 2025.9.1 pyhcf101f3_0 conda-forge
jupyter_core 5.9.1 pyhc90fa1f_0 conda-forge
k8 1.2 he8db53b_6 bioconda
kernel-headers_linux-64 5.14.0 he073ed8_3 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.45 default_hbd61a6d_104 conda-forge
libabseil 20240116.2 cxx17_he02047a_1 conda-forge
libblas 3.11.0 5_h4a7cf45_openblas conda-forge
libcblas 3.11.0 5_h0358290_openblas conda-forge
libcurl 8.17.0 h4e3cde8_1 conda-forge
libdeflate 1.25 h17f619e_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
libexpat 2.7.3 hecca717_0 conda-forge
libffi 3.5.2 h9ec8514_0 conda-forge
libgcc 15.2.0 he0feb66_16 conda-forge
libgcc-ng 15.2.0 h69a702a_16 conda-forge
libgfortran 15.2.0 h69a702a_16 conda-forge
libgfortran5 15.2.0 h68bc16d_16 conda-forge
libgomp 15.2.0 he0feb66_16 conda-forge
liblapack 3.11.0 5_h47877c9_openblas conda-forge
liblapacke 3.11.0 5_h6ae95b6_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
libnghttp2 1.67.0 had1ee68_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_4 conda-forge
libprotobuf 4.25.3 hd5b35b9_1 conda-forge
libsqlite 3.51.1 h0c1763c_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.2.0 h934c35e_16 conda-forge
libstdcxx-ng 15.2.0 hdf11a46_16 conda-forge
libuuid 2.41.2 h5347b49_1 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
markupsafe 3.0.3 py311h3778330_0 conda-forge
mashmap 3.1.3 pl5321hb4818e0_2 bioconda
meryl 1.4.1 h9948957_2 bioconda
minimap2 2.30 h577a1d6_0 bioconda
nbformat 5.10.4 pyhd8ed1ab_1 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.6.1 pyhcf101f3_0 conda-forge
numpy 2.3.5 py311h2e04523_0 conda-forge
openblas 0.3.30 pthreads_h6ec200e_4 conda-forge
openssl 3.6.0 h26f9b46_0 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
parasail-python 1.3.4 py311hc84137b_5 bioconda
perl 5.32.1 7_hd590300_perl5 conda-forge
pip 25.3 pyh8b19718_0 conda-forge
platformdirs 4.5.1 pyhcf101f3_0 conda-forge
protobuf 4.25.3 py311hbffca5d_1 conda-forge
psutil 7.1.3 py311haee01d2_0 conda-forge
pulp 2.7.0 py311h38be061_1 conda-forge
pyparsing 3.2.5 pyhcf101f3_0 conda-forge
pysam 0.23.3 py311hb456a96_1 bioconda
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.11.14 hd63d673_2_cpython conda-forge
python-fastjsonschema 2.21.2 pyhe01879c_0 conda-forge
python_abi 3.11 8_cp311 conda-forge
pyyaml 6.0.3 py311h3778330_0 conda-forge
readline 8.3 h853b02a_0 conda-forge
referencing 0.37.0 pyhcf101f3_0 conda-forge
requests 2.32.5 pyhd8ed1ab_0 conda-forge
reretry 0.11.8 pyhd8ed1ab_1 conda-forge
rpds-py 0.30.0 py311h902ca64_0 conda-forge
samtools 1.22.1 h96c455f_0 bioconda
seqtk 1.5 h577a1d6_1 bioconda
setuptools 80.9.0 pyhff2d567_0 conda-forge
smart_open 7.5.0 pyhcf101f3_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
sysroot_linux-64 2.34 h087de78_3 conda-forge
tabulate 0.9.0 pyhcf101f3_3 conda-forge
throttler 1.2.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_ha0e22de_103 conda-forge
toposort 1.10 pyhd8ed1ab_1 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
typing_extensions 4.15.0 pyhcf101f3_0 conda-forge
tzdata 2025c h8577fbf_0 conda-forge
urllib3 2.6.2 pyhd8ed1ab_0 conda-forge
verkko 2.3 h03b467c_0 bioconda
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
winnowmap 2.03 h5ca1c30_4 bioconda
wrapt 2.0.1 py311h49ec1c0_1 conda-forge
yaml 0.2.5 h280c20c_3 conda-forge
yte 1.9.4 pyhd8ed1ab_0 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forgeverkko -d <work-directory> --hifi <hifi-read-files> [--nano <ont-read-files>]