From c1f99a0281d782459a33f1af2dddbfebb5e0e03c Mon Sep 17 00:00:00 2001 From: Julie ORJUELA Date: Wed, 31 Jan 2024 16:53:47 +0100 Subject: [PATCH] Update README.rst migrating to gitlab!! --- README.rst | 89 ++---------------------------------------------------- 1 file changed, 2 insertions(+), 87 deletions(-) diff --git a/README.rst b/README.rst index dcd39f5..9e19b36 100644 --- a/README.rst +++ b/README.rst @@ -3,90 +3,5 @@ :align: center -|PythonVersions| |SnakemakeVersions| |Singularity| |Downloads| - -.. contents:: Table of Contents - :depth: 2 - -About CulebrONT -=============== - -|readthedocs| - -**Homepage:** `https://culebront-pipeline.readthedocs.io/en/latest/ `_ - -Using data from long reads obtained by Oxford Nanopore Technologies -sequencing makes genome assembly easier, in particular to solve repeats -and structural variants, in prokaryotic as well as in eukaryotic -genomes, resulting in increased contiguity and accuracy. - -Bunch of softwares and tools are released or updated every week, and a -lot of species see their genome assembled using those. - -That’s right. - -“*But which assembly tool could give the best results for my favorite -organism?*” - -**CulebrONT can help you!** CulebrONT is an open-source, scalable, -modulable and traceable snakemake pipeline, able to launch multiple -assembly tools in parallel and providing help for choosing the best -possible assembly between all possibilities. - -Citation -________ - -https://doi.org/10.1101/2021.07.19.452922 - -Authors -_______ - -* Julie Orjuela (IRD) -* Aurore Comte(IRD) -* Sébastien Ravel(CIRAD), -* Florian Charriat(INRAE) -* Sébastien Cunnac(IRD). -* Tram Vi (IRD, AGI) -* Francois Sabot(IRD) - -Useful notes -============ - -Before launching CulebrONT, you could base-calling of arbitrarily -multiplexed libraries across several Minion runs with sequencing quality -control and gather the output files by genome for subsequent steps. For -that use https://github.com/vibaotram/baseDmux. - -Thanks -====== - -Thanks to Ndomassi Tando (i-Trop IRD) by 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 -======= - -Licencied under `CeCill-C `_ and GPLv3. - -Intellectual property belongs to `IRD `_ , `CIRAD `_ and authors. - -.. |PythonVersions| image:: https://img.shields.io/badge/python-≥3.6%2B-blue - :target: https://www.python.org/downloads - -.. |SnakemakeVersions| image:: https://img.shields.io/badge/snakemake-≥6.10.0-brightgreen.svg - :target: https://snakemake.readthedocs.io - -.. |Singularity| image:: https://img.shields.io/badge/singularity-≥3.3.0-7E4C74.svg - :target: https://sylabs.io/docs/ - -.. |readthedocs| image:: https://pbs.twimg.com/media/E5oBxcRXoAEBSp1.png - :target: https://culebront-pipeline.readthedocs.io/en/latest/ - :width: 400px - -.. |Downloads| image:: https://img.shields.io/pypi/dm/culebrONT?color=purple&logo=culebrONT-pypi - :target: https://pypi.org/project/culebrONT - :alt: PyPi downloads +CulebrONT has migrated to https://forge.ird.fr/diade/culebront_pipeline from version 3.0.0 !!! +**********************************************************************************************