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 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

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:

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.

Examples

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 bluesky =)

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