HA1 Deep mutation scanning

Dependencies

• python (version 3.9)
• snakemake
• flash
• seqtk
• cutadapt
• pandas
• biopython

Input files

• All raw reads in fastq format should be placed in fastq/

Dependencies installation

1. Install dependencies by conda:

conda create -n HA1 -c bioconda -c anaconda -c conda-forge \
  python=3.9 \
  seqtk \
  flash \
  biopython \
  cutadapt \
  snakemake

2. Activate conda environment:
   source activate HA1

Calling mutations from sequencing data

1. Using UMI to correct sequencing errors:
   python script/Dedup_UMI.py fastq NNNNNNN 0.8 2

2. Counting mutations:
   snakemake -s HA1_pipeline.smk -j 10