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Pavel V. Dimens edited this page May 16, 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 successor to LepMapp3r, which itself is a wrapper for Lep-Map3 by Pasi Rastas. As I'm sure you've already guessed, the name is derived from Lep-Map3 ("Lep_3") and Snakemake ("Make"). Since Lep-Map3 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 Lep-Map3, 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 Lep-Map3 (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

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