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.yamlCitation
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
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.
3 maintainers
Metadata
3 maintainers
Release files for culebrONT 5.0.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| culebront-5.0.1.tar.gz | 1.8 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| culebront-5.0.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 2.0 MB
Release files / culebront-5.0.1.tar.gz
| Download URL | culebront-5.0.1.tar.gz |
|---|---|
| Size | 1.8 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
e2c45493c0acf96f74817680d4f50803d13b1873b16fa11a96f83184fbc557e2
|
|
BLAKE2b-256 checksum How to use checksums |
4ed0d844de22e8a818427ab32ec983a56971e443e13236bdc0be812b88ff5556
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.12.3
|
Release files / culebront-5.0.1-py3-none-any.whl
| Download URL | culebront-5.0.1-py3-none-any.whl |
|---|---|
| Size | 183.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
55f96d098518687ed77bac4d0d84d3634c938239c7b72a3f0974894faea0acdc
|
|
BLAKE2b-256 checksum How to use checksums |
3ed2633de045bf34f1642911a14f6cb4b015827d257d538d58147681bc271a3f
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.12.3
|
