SARS-CoV-2 amplicon sequencing scripts

• Repo contains code to:

  1. Assemble SC2 amplicon sequences using the V2, V3, VarSkip, and Midnight primer kits
     • Mainly useful for running on an HPC using Linux and SLURM workload manager
  2. Perform QC and amplicon drop-out analysis
     • Useful for getting a snap-shot of sequencing quality and possible amplicon drop-out issues

• Repo is currently in progress

ancov-pipeline.sh

• Script to run the artic-ncov2019 pipeline on data generated using commonly used kits on an HPC
  • This will need to be run with the sayf-artic environment activated; can be done using conda env create -f sayf-artic.yml

Quick usage

• ``

consensus-stats.py

• Script to perform a QC of consensus sequences and check for long stretches of N's or possible drop out issues

Quick usage

• ./run-stats.py -c midnight-consensus-seqs.fa -l 1000 --kit midnight -o ./mid-consensus-qc.png

amp-drop-analysis.py

• Script to check for amplicon drop-outs given a primer scheme, primer reference, and FASTA/multi-FASTA
  1. Prints out alignments for partial primer matches if they exist or notifies you if no match exists for a primer
  2. Generate a plot of the percentage of samples an amplicon does not match
     • Example plot:
     

Quick usage

• ./amp-drop-analysis.py -b ~/Documents/TestSpace/midnight/V1/midnight.scheme.bed -r ~/Documents/TestSpace/midnight/V1/midnight.reference.fasta -c ~/Documents/SC2Genomes/Broad-consensus.mfa

  • Example output from above command:

• ./amp-drop-analysis.py -b ~/Documents/TestSpace/midnight/V1/midnight.scheme.bed -r ~/Documents/TestSpace/midnight/V1/midnight.reference.fasta -c ~/Documents/SC2Genomes/Broad-consensus.mfa --text-print | less

  • The --text-print option removes colors from the print-outs and allows for neatly saving output in a text file
  • Example output from above command: