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Welcome to the SLIMM wiki

SLIMM is a short for Species Level Identification of Microbes from Metagenomes. As the name suggests it is a taxonomic identification 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.

There are three ways to install SLIMM.

1. Install using conda (Linux and MacOs only) conda install -c bioconda slimm
2. Download pre-compiled Binaries or
3. Build from source.

In order to successfully run SLIMM follow the following steps: (More hands-on tutorials are provided based on yara-mapper (here) and bowtie2 (here )

1. Download already indexed reference genomes for Archaea, Bacteria Fungi and Viral groups. (Indexed reference genomes of Archaea, Bacteria Fungi and Viral groups are provided for Yara and Bowtie2 read mappers.) If you want to use your own custom database follow the instructions provided here.

2. After doing the necessary quality control on your metagenomic sequences map them to the (indexed) reference genomes. Configure your read mapper to output secondary alignments. For example, you can use --strata-rate 1 for yara-mapper and -k 30 for bowtie2.

3. Download SLIMM databases from here. Make sure the size of the SLIMM database (5K or 13K) matches the size of the reference genomes you downloaded.

4. Now you can run SLIMM on the SAM/BAM file you obtained from step 2. For example,

    ./bin/slimm -w 1000 -o slimm_reports/ slimm_db_20180924.sldb MG_0001.bam 
   

The resulting taxonomic profile will be stored in the same directory as the input SAM/BAM file. For more options, you can run slimm with -h option.

Read the following to get more insight about how to use the SLIMM.

FAQ

Download Binaries

Build from source

Preparing a custom database

Example using yara-mapper

Example using Bowtie2