This Workflow was modified from the Snakemake workflow provided by phiweger of Nanotext, and with help from C. Titus Brown and Luiz Irber from the dib-lab

Running the Workflow

To run the workflow:

Sequencing Reads

Create symbolic links to paired read files in reads/.

Config File

To setup HMM database:

Navigate to the directory where you wish for the database to live

Use wget and hmmer v3.1b

# download and set up HMM database
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam32.0/Pfam-A.hmm.gz
gunzip Pfam-A.hmm.gz
hmmpress Pfam-A.hmm

Then, set the absolute path for the pfam database on the system in config.json.

Execute

Execute the following using this folder as the working directory:

snakemake -j 100 \
--cluster-config cluster.json \
--cluster "sbatch -A {cluster.account} \
--mem={cluster.mem} -t {cluster.time} \
-c {threads}" \
--configfile config.json \
--use-conda

The results/ folder will be created with genome annotations in data/ and a log/ if anything goes wrong.

When running this workflow, check for concordance between the file extension of input read files and code in the Snakefile.