SARS-CoV-2-leader notebook wrapper

A jupyter notebook wrapper for the SARS-CoV2-leader scripts (https://github.com/achamings/SARS-CoV-2-leader). Please see ./notebooks/covid19_leader.ipynb for more information.

Requirements

• conda

Installation

install conda env, recommendation is into project dir conda create env -p ./.venv -f ./notebooks/covid19_leader.conda.env.yml

Set the jupyter server to use the conda env install conda env, recommendation is into project dir by pointing it to./.venv

Add associate input and output folders. The default location is ./input and ./output,

• input
  • The resulting mapped bam files for each smaple against the SARS-CoV2 reference genome.
  • (Optional) indexed bam file .bam.bai, this provides additional statistics with the base program, however, none of these values are used for the notebook.
• output
  • Each sample has the following files:
    • .bam/.bai: A bam file containing only reads with the leader sequence.
    • .depth.txt: A tsv file containing the depth at each position at the specified Q value.
    • .csv (unused): A csv file containing average coverage before and after (often empty).
    • .sam (unused): A sam file containing only reads with the leader sequence.
    • .txt (unused): The output of the original program on the single sample
  • COVID_leader_splice_sites.tsv: A tsv file containing the counts of each reads on the selected positions
  • COVID_leader_splice_sites.proportional.tsv (final data output): Contains the previous file content and calculates the proportion of each site per sample as well

NOTE: for ./sars_cov2_leader.sh to work on mac you'll also need to install md5sum (e.g. brew install md5sha1sum)