Hello
In their 2016 Genetics paper, Maria Doitsidou et al. provided a workflow for mapping-by-sequencing: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068839/figure/fig4/.
Some of the constituent tools are no longer maintained. Does anyone know of an up to date pipeline to use in Galaxy for NGS analyses of re-sequenced C. elegans mutants?
Thanks
There is MiModD (https://celegans.de/mimodd/), our standalone tool suite for Galaxy or command-line use.
It will become the official replacement (https://biostar.usegalaxy.org/p/26130/) for CloudMap on Galaxy Main
very soon (within the next two weeks, hopefully), but if you are talking about your own instance of Galaxy you
can go ahead and use it right now (several labs have already done so succesfully).
Best,
Wolfgang