SLIMM - Species Level Identification of Microbes from Metagenomes
a taxonomic profiling tool that investigates which microorganisms are present in a sequenced sample. SLIMM requires a BAM/SAM alignment file as an input. One can use a read mapper of choice to map raw reads obtained from a sequencing machine to obtain the BAM/SAM file required as input for SLIMM.
slimm_build [OPTIONS] -nm names.dmp -nd nodes.dmp FASTA_DB nucl_gb.accession2taxid slimm [OPTIONS] $SLIMM_DB_PATH $SAM_FILE_PATH Try 'slimm --help' for more information.
* SLIMM version: 0.3.0 * Last update: February 2018
Pre-built executables for Linux and Mac are made available at the releases page.
You can build SLIMM from its source. Instruction on how to build from source can be found at the [slimm wiki] (https://github.com/seqan/slimm/wiki)
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 https://doi.org/10.7717/peerj.3138