Metagenome assembled genome workflows

If you do not have conda installed on the account then navigate to: https://docs.conda.io/en/latest/miniconda.html and install miniconda for linux 64 bit. **Right click and select COPY ADDRESS. **Navigate to your terminal and type:

#Miniconda.sh is the file downloaded from the copy address
wget <copied address>
chmod +x Miniconda.sh 
./Miniconda.sh

Slurm scripts to run basic QC and annotation

Setting up a conda environement

conda create -n metagenome
conda activate metagenome
conda install -c conda-forge mamba

Setting up packages in conda environment

mamba install -c bioconda prinseq-plus-plus==1.2.3
mamba install -c bioconda kraken2 
mamba install -c bioconda super-focus 

Setting up the input data

** For now this workflow runs only on illumina paired end **

#create a directory - reads 
mkdir paired
#drop forward and reverse reads here


#If the reads are already on the cluster elsewherre, just symlink the data
ln -s /scratch/user/nal/ scratch

#save the sample names to a file
ls paired/ | grep "R1.fastq.gz" | sed -e 's/_R1.fastq.gz//g'  > sample-names.txt