Documentation: https://culebront.readthedocs.io/en/latest/

Which assembler gives the best genome for my organism? CulebrONT runs several long-read assemblers side by side on the same reads (Canu, Flye, hifiasm, Miniasm, NextDenovo, Raven, Shasta, SmartDenovo), polishes and corrects their assemblies (Racon, Medaka, Pilon), evaluates them (BUSCO, QUAST, Merqury, BlobToolKit, Assemblytics, GCI, LAI, GenomeScope2…) and compares them in one offline HTML report. It is a Snakemake workflow that runs on a single machine or on a Slurm cluster, with an apptainer image or the cluster modules.

python3 -m pip install culebrONT
culebrONT install --mode local                       # or: culebrONT install (Slurm)
culebrONT test --dataset ecoli -d ~/culebrONT_test
culebrONT run -c ~/culebrONT_test/data_test_config_ecoli.yaml
# choose the assemblies to evaluate in OUTPUT/assembly_selection.tsv, then:
culebrONT quality -c ~/culebrONT_test/data_test_config_ecoli.yaml

Citation

Orjuela J, Comte A, Ravel S, Charriat F, Vi T, Sabot F, Cunnac S. CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes. https://doi.org/10.1101/2021.07.19.452922

Authors

Maintainers: Julie Orjuela (IRD), Aurore Comte (IRD), Sébastien Ravel (CIRAD).

Authors: Julie Orjuela (IRD), Aurore Comte (IRD), Sébastien Ravel (CIRAD), Florian Charriat (INRAE), Tram Vi (IRD, AGI), François Sabot (IRD) and Sébastien Cunnac (IRD).

Thanks

Thanks to Ndomassi Tando (i-Trop IRD) for the administration support.

The authors acknowledge the IRD i-Trop HPC (South Green Platform) at IRD Montpellier for providing HPC resources that have contributed to this work.

Thanks to Yann Delorme for this beautiful logo.

License

Licensed under CeCill-C and GPLv3.

Intellectual property belongs to IRD, CIRAD and authors.

Metadata

Release files for culebrONT 5.0.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for culebrONT 5.0.0
File	Size	Uploaded
culebront-5.0.0.tar.gz	1.8 MB	Oct 9, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for culebrONT 5.0.0
File	Interpreter	ABI	Platform	Reset
culebront-5.0.0-py3-none-any.whl 182.1 kB Oct 9, 2026	Python 3	none	any	Details

Total release size: 2.0 MB

Release files / culebront-5.0.0.tar.gz

Download URL	culebront-5.0.0.tar.gz
Size	1.8 MB
Tags	Source
SHA-256 checksum How to use checksums	`eba4618d5991eb96fd138f85a9f1c9a5fea593247eea9916f4ffed0dd1b201b0`
BLAKE2b-256 checksum How to use checksums	`437d016ad752360a0f2eca78830a1ef27e7b546dbecef767d4a8c57d2f971aba`
Upload date	Oct 9, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.3`

Release files / culebront-5.0.0-py3-none-any.whl

Download URL	culebront-5.0.0-py3-none-any.whl
Size	182.1 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`4a1c251a13abc8029754d514b79088d1954b133ddd1cc56765139f9b8a8946f0`
BLAKE2b-256 checksum How to use checksums	`0aad76ec6025eaafa1fe1a97684be133c147bc4fffff4dbbc7266a4f9ca9f90b`
Upload date	Oct 9, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.3`