Please do use the LotuS2 github at the moment, while we are preparing a stable release candidate.
The latest release can be found here:
The use of LotuS2 is free for academic, non-commercial research purposes. Please read the LotuS2 license.
SDM is at the heart of LotuS2 and is responsible for demultiplexing, quality filtering and dereplication of the amplicon reads. In the following github folder you will find configuration files for different sequencing platforms and software configurations that LotuS and SDM use.
Config files: https://github.com/hildebra/lotus2/tree/master/configs
Mice faecal samples & mapping
The finished LotuS2 run with these files with default settings:
Finished LotuS2 run
All above files: miSeq.tar.gz
Human (hg38): http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/