From bb0fd6ab9b5e93426b1737449f68f4d1ea77e7ee Mon Sep 17 00:00:00 2001 From: "Pavel V. Dimens" Date: Thu, 20 May 2021 11:40:54 -0400 Subject: [PATCH 1/4] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 13cde6c..c2a233f 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ ![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) From ff06927cc2930ba838d6b0a482b80672bc8cc576 Mon Sep 17 00:00:00 2001 From: "Pavel V. Dimens" Date: Thu, 20 May 2021 11:44:23 -0400 Subject: [PATCH 2/4] Update README.md --- README.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index c2a233f..6009e94 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ _It's Lep-Map3, but with snakes_ 🐍🐍 # 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. @@ -39,10 +39,12 @@ where `` is an integer of the maximum number of cores/threads y ### Something to keep in mind -Lep-Map3 is a **very** comprehensive software, and LepWrap doesn't incorporate all the features and nuances. Your study is unique, so you are encouraged to clone or fork this repo 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. If using LepWrap in a publication, cite **Pasi Rastas** for his work on Lep-Map3 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) =) +Lep-Map3/Anchor are **very** comprehensive software, and LepWrap doesn't incorporate all the features and nuances. Your study is unique, so you are encouraged to clone or fork this repo and adapt LepWrap to your needs! All of the code in LepWrap is written as human-readable as possible and aggressively annotated, so give it a shot and adapt it to your workflow. If using LepWrap in a publication, cite **Pasi Rastas** for his work and please include a link to it in your publication. If you like using it, star this repository and 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) 😊 ## Citation 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 From a863e3e49f84ee86e377b7ca5b0f42ba5e8d804a Mon Sep 17 00:00:00 2001 From: "Pavel V. Dimens" Date: Thu, 20 May 2021 13:00:30 -0400 Subject: [PATCH 3/4] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 6009e94..70fd03e 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ git clone https://github.com/pdimens/LepWrap.git Assuming you have `anaconda` or `miniconda` installed: ```bash cd LepWrap -conda create -f conda_LepWrap.yml +conda create -f conda_setup.yml ``` This will create an environment called `lepwrap` that can be activated with: ```bash From 0d1dc8081fc6d141adb0fc935366662b97085e36 Mon Sep 17 00:00:00 2001 From: "Pavel V. Dimens" Date: Thu, 20 May 2021 13:01:42 -0400 Subject: [PATCH 4/4] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 70fd03e..cad906c 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ git clone https://github.com/pdimens/LepWrap.git Assuming you have `anaconda` or `miniconda` installed: ```bash cd LepWrap -conda create -f conda_setup.yml +conda create -f conda_setup.yml -n lepwrap ``` This will create an environment called `lepwrap` that can be activated with: ```bash