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LepWrap is a wrapper for LepMap3 (Rastas 2017) and LepAnchor (Rastas 2020) intended to link the modules together into a single workflow.

Since Lep-Map3/Anchor themselves are composed of several Java modules and external scripts, it only made sense to combine them into a deterministic modular workflow. LepWrap does not include every module and option available to Lep-Map3 or LepAnchor, but it covers the essentials and the improved legibility and modularity of Snakemake framework makes it a lot easier to adapt and modify to your needs.

Citation

If using LepWrap and publishing, cite Pasi Rastas for his work on Lep-Map3 and Lep-Anchor, and if you like using it, star this repository and give me a shout out on Twitter @pvdimens ! 😊

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