README.md

gradient_viral

Quickstart

1. Grab the code

$ git clone git@github.com:MGXlab/gradient_virome.git 
$ conda create -n gradient_virome --file conda-linux-64.lock
$ conda activate gradient_virome

2. Define a tab-separated samplesheet with a header and column names

• sample_id
• pair_id: mucosal and luminal paired id
• gradient: mucosal or luminal (can be anything really)
• R1: Path to forward fastq file
• R2: Path to reverse fastq file
• R1_MD5: MD5 numbers of Generated R1 FASTQ files
• R2_MD5: MD5 numbers of Generated R2 FASTQ files
• compartment: almond: 0-rhizosphere, 1-bulk soil; sponge: 0-sponge, 1-seawater; gut: 0-lumen, 1-mucosa.

3. Fill in the config.yaml based on your needs.

4. Execute from within this dir.

5. Datasets:

   • almond: https://www.researchgate.net/publication/371360764_Almond_rhizosphere_viral_prokaryotic_and_fungal_communities_differed_significantly_among_four_California_orchards_and_in_comparison_to_bulk_soil_communities
   • sponge: https://www-sciencedirect-com.proxy.library.uu.nl/science/article/pii/S1931312819304287#sec4
   • mammalian gut: https://www.nature.com/articles/s41564-022-01178-w

# This is a dry run
(gradient_virome)$ snakemake -j 94 --use-conda --conda-frontend mamba -p -n

• Remove -n to run it

Input

Short, paired-end sequencing reads of a sample.