SLIMM – Species Level Identification of Microbes from Metagenomes

SLIMM is a taxonomic profiling tool that investigates which microorganisms are present in a sequenced sample. SLIMM uses coverage landscape of reference genomes by sequencing reads to remove unlikely genomes from the analysis and subsequently gain more uniquely-mapped reads to assign at lower ranks of a taxonomic tree. This approach enables SLIMM to be sensitive in predicting members of a microbial community while maintaining a low false positive rate. It has been also shown that SLIMM predicts the relative abundances of individual members with lower deviation from the actual relative abundances compared to other methods. SLIMM requires a BAM/SAM alignment file as an input. One can use a read mapper of choice to map raw sequencing reads to obtain the BAM/SAM alignment file required as input for SLIMM.

Getting Started

More details on how to use SLIMM can be found at the SLIMM WIKI



Pre-built executables for Linux and Mac are made available at the RELEASE PAGE .


You may download already INDEXED REFERENCE GENOMES for Bacteria and Archaea groups. (Indexed reference genomes of Bacteria and Archaea groups are provided for Yara and Bowtie2 read mappers.) If you want to use your own custom database follow the instructions provided here.

Source code

You can build SLIMM from its source. Instruction on how to build from source can be found at the SLIMM WIKI

Cite us

If you use SLIMM in your work-flows, don’t forget to cite us.

Dadi TH, Renard BY, Wieler LH, Semmler T, Reinert K. (2017) SLIMM: species level identification of microorganisms from metagenomes. PeerJ 5:e3138


For questions, comments, or suggestions please contact:

Temesgen H. Dadi