LotuS2 Pipeline

The latest release can be found here, with "git pull" you will also get minor updates inbetween big releases.

You can also install LotuS2 via conda:

And via docker:

Docker Image

And is available for Galaxy (search for LotuS2 in Tools):


The use of LotuS2 is free for academic, non-commercial research purposes. Please read the LotuS2 license.

Additional Files

Config files

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:

454 Tutorial Files

Original 454 files from mice ceacal experiment (published in Hildebrand et al, 2013):

Mice faecal samples & mapping

The finished LotuS2 run with these files with default settings:

Finished LotuS2 run

miSeq Example Files

This run was specifically created to test the validity of sequencing pipelines using technical replicates of human feacal samples.

Run1: MIDs, Pair1, Pair2

Run2: MIDs, Pair1, Pair2

Mapping file

All above files: miSeq.tar.gz

Host Genomes

Reference host genomes for the --offtargetDB option
host genomes

Human (hg38):


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