ViromeDataProcessing

Central codebase for virome data processing pipeline

Step 0 - Set up and fetch raw data

Installing Conda

Personally, I'm going to try micromamba:

https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html

curl micro.mamba.pm/install.sh | bash

Setting up the ViromeProcessing conda environment

micromamba create -n ViromeDataProcessing -f ViromeDataProcessing.yml

Non-conda resources

Follow these instructions to install bbtools https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/installation-guide/

Step 0 - Get data and verify

Run the following command:

conda activate ViromeDataProcessing

Download raw data

For people wanting to reproduce this analysis post publication, download raw reads from the SRA

For me, I copied the data from the UC Davis Genome Center server into

Run 0-preprocessing.smk

This has the option of merging multiple runs and runs FastQC and MultiQC