Authors Wolfgang Maier, Mark Seifert, Katharina Moos, Ralf Baumeister, University of Freiburg
Abstract MiModD (http://www.celegans.de/mimodd) is a GPLv3-licensed comprehensive tool suite for variant mapping and identification. It extends ideas and concepts found in CloudMap, for which it can serve as a drop-in replacement. Package highlights include: i) a fully integrated mapping-by-sequencing analysis pipeline without external dependencies, ii) multisample variant calling and filtering for improved call statistics and straightforward variant identification, iii) NacreousMap linkage analysis and plotting engine with full compatibility, but improvements over CloudMap. While MiModD can be installed and used as a standalone package for command line use, it features a full set of tool wrappers for seamless integration into Galaxy and is also available from the Galaxy Main Tool Shed (https://toolshed.g2.bx.psu.edu/view/wolma/mimodd). For users who just want to take advantage of the NacreousMap plotting engine to replot their existing CloudMap analyses, we host a dedicated public Galaxy server at http://mapping-by-sequencing.vm.uni-freiburg.de:8080.