README

⚠️ This a pipeline to produce RenSeq assemblies using snakemake.

Requirements:

• git
• conda
• snakemake
• At least 15 cores CPU

To run this pipeline:

1. Clone this repository in the machine that will be providing the hardware. You need to have git installed in this machine:

   git --version
   git clone https://github.com/cahuparo/renseq_assembly_snakemake.git

2. Create the conda environment to makesure that all tools/packages are installed:

   conda create --prefix /path/to/the/working/directory/env_renseq_assembly
   conda activate /path/to/the/working/directory/env_renseq_assembly
   conda install -c bioconda snakemake
   conda install -c bioconda pbccs
   conda install -c bioconda bamtools
   conda install -c bioconda bam2fastx
   conda install -c bioconda cutadapt
   conda install -c bioconda blasr
   conda install -c bioconda biopython
   conda install -c bioconda canu
   conda deactivate

3. Gather raw data (bam file) for each genotype and place it in a directory labeled bam

   mkdir bam
   #cp or scp bam files ---> to the bam directory

4. Then create a screen session

   screen

5. Activate conda environment

   conda activate /path/to/the/working/directory/env_renseq_assembly

6. Run snakemake and monitor after control + AD

   snakemake --latency-wait 120 --cores 32