Example yara mapper

This tutorial works with slimm version 0.3.0 or higher. For earlier versions use the old tutorial instead.

1. Install slimm using your method of choice. We recommend conda. conda install -c bioconda slimm

   Other choices are:

   • Download pre-compiled Binaries or
   • Build from source.

2. Create a fresh directory called slimm_tutorial

    mkdir ~/slimm_tutorial
    cd ~/slimm_tutorial
   

3. Download and extract the viruses only version yara index (V_genomes_indices_20180924_yara.zip) from here. This yara index contains reference genome database of different viral species.

    wget https://ftp.mi.fu-berlin.de/pub/dadi/slimm/V_genomes_indices_20180924_yara.zip
    unzip V_genomes_indices_20180924_yara.zip 
   

4. Download the corresponding SLIMM database (slimm_db_20180924.sldb) from here. The same SLIMM database can be used for other groups such as Archea Bacteria Fungi and Viral as well as their combinations.

    wget https://ftp.mi.fu-berlin.de/pub/dadi/slimm/slimm_db_20180924.sldb
   

5. Create two new directories with the name alignment_files slimm_reports and place your metagenomic sequencing reads under a directory named mg_reads . If you don't have one yet, you may download SRR1057982 and use it. Now you should have the following folder/directory structure in your working directory:

      Working Directory
      │
      ├── V_genomes_indices_20180924_yara (indexed reference genomes)
      ├    ├── V_genomes.lf.drs
      ├    ├── V_genomes.lf.drv 
      ├    ├── V_genomes.rid.concat
      ├    ├── ...
      │
      ├── slimm_db_20180924.sldb (SLIMM taxonomic database)
      │
      ├── alignment_files (alignment files will be stored here)
      │
      ├── slimm_reports (slimm taxonomic reports will be stored here)
      │
      ├── mg_reads (metagenomic sequencing reads) 
      ├    ├── SRR1748536_1.fastq
      ├    ├── SRR1748536_2.fastq
   

6. Use yara-mapper to map the metagenomic reads against reference genomes and produce alignment files.

    yara_mapper -v -t 30 -s 2 -sa record \
            -o ./alignment_files/SRR1748536.bam \
            .V_genomes_indices_20180924_yara/V_genomes \
            ./mg_reads/SRR1748536_1.fastq \
            ./mg_reads/SRR1748536_2.fastq \
   

7. Run SLIMM on the output of the read mapper (SAM/BAM files)

    slimm -w 1000 \
          -o slimm_reports/ \
           slimm_db_20180924.sldb \
           alignment_files/SRR1748536.bam
   

You will find a taxonomic profile of your sample under the directory slimm_reports/ with the name SRR1748536_profile.tsv. The file contains a multi-level taxonomic profile of the sample that SLIMM reported. The first column indicates the taxonomic rank for easy filtering.

You can also tell SLIMM to report only a single rank using -r parameter. For example,

    slimm -w 1000 -r species \
          -o slimm_reports/ \
           slimm_db_20180924.sldb \
           alignment_files/SRR1748536.bam

Would generate species level report only.

(see slimm --help for more details)