virus_identification_tools_benchmarking

Quickstart

1. Grab the code

$ git clone [email protected]:MGXlab/virus_identification_tools_benchmarking.git 
$ conda create -n virbench --file conda-linux-64.lock

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

• sample_id
• pair_id: microbial and viral paired id
• fraction: viral or microbial (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

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

4. Execute from within this dir.

# This is a dry run
(virbench)$ snakemake -j 32 --use-conda --conda-frontend mamba -p -n

• Remove -n to run it

Input

Short, paired-end sequencing reads for the viral and microbial fraction of a sample. The fraction information must be provided in the samplesheet.