LepWrap is a reusable pipeline to use the linkage map software Lep-Map3 and the genome assembly map-based anchoring and orienting software Lep-Anchor. Check out the documentation/wiki for detailed installation, usage, and workflow information.
How to install
You will need a conda installation (Anaconda or Miniconda, I recommend Miniconda). Alternatively, you can download latest release or clone this repository locally (see wiki)
Create an environment called lepwrap and install LepWrap into it in a single command.
conda create -n lepwrap -c bioconda lepwrap
Activate the environment with conda activate lepwrap
This can also be done in an environment of your choosing
You will need to modify config.yml to suit your needs, then you can simply run the pipeline with the wrapper:
LepWrap <number_of_cores> <config.yml>
where <number_of_cores> is an integer of the maximum number of cores/threads you want the pipeline to use and <config.yml> (optional!) is the name of the config file, if it’s different than config.yml. If no config file is found in the directory, LepWrap will generate a default one for you to edit.
LepWrap does things a certain way, employing the most common/reasonable way of using Lep-Map3 (and LepAnchor, more or less). The current version is a lot more flexible that its predecessors, but might still lack something you need. Your study is unique, and I encourage you to clone/fork this repository and adapt LepWrap to it! 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 welcome!
Citation
If using LepWrap in a publication, cite Pasi Rastas for their work on Lep-Map3/Lep-Anchor and cite this repository using the Zenodo citation. You are also encouraged to cite LepWrap if you just use the edge-trimming part of it. If you like LepWrap, please Star the repository and/or give me (Pavel) a shout out on social media mastodonbluesky =)
It’s Lep-Map3 and Lep-Anchor, but with snakes 🐍🐍
LepWrap
LepWrap is a reusable pipeline to use the linkage map software Lep-Map3 and the genome assembly map-based anchoring and orienting software Lep-Anchor. Check out the documentation/wiki for detailed installation, usage, and workflow information.
How to install
You will need a
condainstallation (Anaconda or Miniconda, I recommend Miniconda). Alternatively, you can download latest release or clone this repository locally (see wiki)Create an environment called
lepwrapand installLepWrapinto it in a single command.Activate the environment with
conda activate lepwrapThis can also be done in an environment of your choosing
How to run
You will need to modify
config.ymlto suit your needs, then you can simply run the pipeline with the wrapper:where
<number_of_cores>is an integer of the maximum number of cores/threads you want the pipeline to use and<config.yml>(optional!) is the name of the config file, if it’s different thanconfig.yml. If no config file is found in the directory, LepWrap will generate a default one for you to edit.Examples
Something to keep in mind
LepWrap does things a certain way, employing the most common/reasonable way of using Lep-Map3 (and LepAnchor, more or less). The current version is a lot more flexible that its predecessors, but might still lack something you need. Your study is unique, and I encourage you to clone/fork this repository and adapt LepWrap to it! 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 welcome!
Citation
If using LepWrap in a publication, cite Pasi Rastas for their work on Lep-Map3/Lep-Anchor and cite this repository using the Zenodo citation. You are also encouraged to cite LepWrap if you just use the edge-trimming part of it. If you like LepWrap, please Star the repository and/or give me (Pavel) a shout out on social media mastodon bluesky =)