https://github.com/pdimens/lepwrap
A pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring and orienting genome assemblies with said linkage maps.
https://github.com/pdimens/lepwrap
bioinformatics genome-assembly linkage linkage-mapping snakemake
Last synced: about 1 month ago
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A pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring and orienting genome assemblies with said linkage maps.
- Host: GitHub
- URL: https://github.com/pdimens/lepwrap
- Owner: pdimens
- Created: 2020-05-01T17:18:28.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2024-02-26T15:23:47.000Z (about 1 year ago)
- Last Synced: 2025-03-25T11:49:16.632Z (about 2 months ago)
- Topics: bioinformatics, genome-assembly, linkage, linkage-mapping, snakemake
- Language: Perl
- Homepage: https://github.com/pdimens/LepWrap/wiki
- Size: 9.73 MB
- Stars: 12
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
_It's Lep-Map3 and Lep-Anchor, but with snakes 🐍🐍_
[](https://github.com/pdimens/LepWrap/wiki)
[](https://doi.org/10.5281/zenodo.6055565)
# LepWrap
LepWrap is a reusable pipeline to use the linkage map software [Lep-Map3](https://sourceforge.net/projects/lep-map3/) and the genome assembly map-based anchoring and orienting software [Lep-Anchor](https://sourceforge.net/p/lep-anchor/wiki/Home/). Check out [the documentation/wiki](https://github.com/pdimens/LepWrap/wiki) for detailed installation, usage, and workflow information.
### How to install
You will need a `conda` installation ([Anaconda](https://docs.anaconda.com/anaconda/install/) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html), 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.
```bash
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
```bash
conda activate some_env
conda install -c bioconda lepwrap
```
### How to run
You will need to modify `config.yml` to suit your needs, then you can simply run the pipeline with the wrapper:
```bash
LepWrap
```
where `` is an integer of the maximum number of cores/threads you want the pipeline to use and `` (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.
**Examples**
```bash
LepWrap 15 # assumes config.yml
LepWrap 32 nojoinsingles.yml # specific config file
```
### 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](https://ecoevo.social/@pvdimens) [bluesky](https://bsky.app/profile/pvdimens.bsky.social) =)
> Pavel V. Dimens. (2022). pdimens/LepWrap: link with zenodo (4.0). Zenodo. https://doi.org/10.5281/zenodo.6055565
> 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