References

REFERENCES

Once you have all necessary Dependencies, specially [NCBI_blast +] (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download), [SAMtools] (http://samtools.sourceforge.net/) and [Bowtie 2] (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml), you can procede to generate the references the pipeline will use. We strongly advise you to get a look at the Directory Structure our pipeline uses before starting to create the references.
You will need a separate reference directory for each organism group you want to analyse and a host reference so all the host reads can be filtered out. Below are links to the wiki guide to generate all the databases.

• Host
• Bacteria
• Virus
• Fungi
• Invertebrate
• Protozoa