Skip to content
Pavel V. Dimens edited this page May 6, 2020 · 11 revisions

LepMak3r is a wrapper for LepMap3 (Rastas 2017) intended to link the modules together into a single workflow.

LepMak3r was created to be a much more sensibly modular update/alternative to LepMapp3r, which itself is a wrapper for LepMap3 by Pasi Rastas. As I'm sure you've already guessed, the name is derived from LepMap3 ("Lep_3") and Snakemake ("Make"). Since LepMap3 itself is composed of several Java modules, it only made sense to combine them into a deterministic modular workflow. Much like LepMapp3r, LepMak3r does not include every module and option available to LepMap3, but the improved legibility and modularity of Snakemake framework makes it a lot easier to adapt and modify to your needs.

Citation

If using LepMak3r and publishing, cite Pasi Rastas for his work on LepMap3 (below), and if you like using it, give Pavel Dimens a shout out on Twitter @pvdimens alt text =)

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

Getting started

LepMap3 Workflow

LepAnchor Workflow

Other

Clone this wiki locally