From 4291aea7ec6ac896cbd073fb238305e6ae16e99d Mon Sep 17 00:00:00 2001 From: Haibao Tang Date: Thu, 13 Jun 2024 06:34:56 -0700 Subject: [PATCH] Update README and citation section (#677) * don't make index * updated webcolors broke * update README --- README.md | 19 ++++++------------- 1 file changed, 6 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 78ec90f2..822accf7 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,5 @@ # JCVI utility libraries -[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.31631.svg)](https://doi.org/10.5281/zenodo.594205) [![Latest PyPI version](https://img.shields.io/pypi/v/jcvi.svg)](https://pypi.python.org/pypi/jcvi) [![bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/jcvi/README.html?highlight=jcvi) [![Github Actions](https://github.com/tanghaibao/jcvi/workflows/build/badge.svg)](https://github.com/tanghaibao/jcvi/actions) @@ -18,24 +17,18 @@ computation related to assembly, annotation, and comparative genomics. | Email | | | License | [BSD](http://creativecommons.org/licenses/BSD/) | -## Citations +## How to cite -- If you use the MCscan pipeline for synteny inference, please cite: - - _Tang et al. (2008) Synteny and Collinearity in Plant Genomes. [Science](https://science.sciencemag.org/content/320/5875/486)_ +> [!TIP] +> JCVI is now published in iMeta! +> +> _Tang et al. (2024) JCVI: A Versatile Toolkit for Comparative Genomics +> Analysis. [iMeta](https://doi.org/10.1002/imt2.211)_ ![MCSCAN example](https://www.dropbox.com/s/9vl3ys3ndvimg4c/grape-peach-cacao.png?raw=1) -- If you use the ALLMAPS pipeline for genome scaffolding, please cite: - - _Tang et al. (2015) ALLMAPS: robust scaffold ordering based on multiple maps. [Genome Biology](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0573-1)_ - ![ALLMAPS animation](https://www.dropbox.com/s/jfs8xavcxix37se/ALLMAPS.gif?raw=1) -- For other uses, please cite the package directly: - - _Tang et al. (2015). jcvi: JCVI utility libraries. Zenodo. [10.5281/zenodo.31631](http://dx.doi.org/10.5281/zenodo.31631)_ - ![GRABSEEDS example](https://www.dropbox.com/s/yu9ehsi6sqifuaa/bluredges.png?raw=1) ## Contents