diff --git a/README.md b/README.md index cae9931..5e59b78 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,13 @@ ![logo](.misc/logo.png) -_It's Lep-Map3, but with snakes 🐍🐍_ + +_It's Lep-Map3, but with snakes_ 🐍🐍 [![alt text](https://img.shields.io/badge/docs-wiki-75ae6c?style=for-the-badge&logo=Read%20The%20Docs)](https://github.com/pdimens/LepWrap/wiki) # LepWrap -LepWrap is a reusable pipeline to use the linkage map software [Lep-Map3](https://sourceforge.net/projects/lep-map3/). It is the Snakemake-based successor to [LepMapp3r](https://github.com/pdimens/LepMapp3r). Check out [the wiki](https://github.com/pdimens/LepWrap/wiki) for detailed installation, usage, and workflow information. +LepWrap is a reusable pipeline to use the linkage map software [Lep-Map3](https://sourceforge.net/projects/lep-map3/) and [Lep-Anchor](https://sourceforge.net/projects/lep-anchor/). It is the Snakemake-based successor to [LepMapp3r](https://github.com/pdimens/LepMapp3r). Check out [the wiki](https://github.com/pdimens/LepWrap/wiki) for detailed installation, usage, and workflow information. @@ -23,7 +24,9 @@ git clone https://github.com/pdimens/LepWrap.git Assuming you have `anaconda` or `miniconda` installed: ```bash cd LepWrap + conda env create -f conda_setup.yml + ``` This will create an environment called `lepwrap` that can be activated with: ```bash @@ -41,9 +44,10 @@ where `` is an integer of the maximum number of cores/threads y LepWrap does things a certain way, employing the most common/reasonable way of using Lep-Map3 (and LepAnchor more or less). Version `3.2+` is **a lot** more flexible that its predecessors, but might still lack something you're looking for. Your study is unique, and I encourage youto clone/fork this repository and adapt LepWrap to your needs! All of the code in LepWrap is written in human-readable bash or aggressively annotated R, so give it a shot and adapt it to your workflow. PR's always welcome! + ## Citation If using LepWrap in a publication, cite **Pasi Rastas** for their work on Lep-Map3/Lep-Anchor and please include a link to this repository. If you like using it, give me (Pavel) a shout out on Twitter [@pvdimens](https://twitter.com/PVDimens) [![alt text](http://i.imgur.com/wWzX9uB.png)](https://twitter.com/PVDimens) =) > Pasi Rastas, Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data, Bioinformatics, Volume 33, Issue 23, 01 December 2017, Pages 3726–3732,https://doi.org/10.1093/bioinformatics/btx494 -> Pasi Rastas, Lep-Anchor: automated construction of linkage map anchored haploid genomes, Bioinformatics, Volume 36, Issue 8, 15 April 2020, Pages 2359–2364, https://doi.org/10.1093/bioinformatics/btz978 +> Pasi Rastas, Lep-Anchor: automated construction of linkage map anchored haploid genomes, Bioinformatics, Volume 36, Issue 8, 15 April 2020, Pages 2359–2364, https://doi.org/10.1093/bioinformatics/btz978 \ No newline at end of file