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Compare multiple samples breseqs

Requirements

  • breseq 0.29.0 (docs)
  • gdtools 0.29.0 (docs)

These can be installed using command: conda install -c bioconda breseq. Best method is to create a conda environment.

Run breseq_compare.sh

Before running breseq_compare.sh provide paths to reference genome in genbank format (gb), and GenomeDiff or .gd files for multiple breseq runs.

QC plots for coronavirus sequencing data using ncov-tools

  • reference: https://github.com/jts/ncov-tools

  • run script prepare_ncov-tools_summaries.sh to generate the plots

  • provide absolute path to results from SIGNAL pipeline example:

./prepare_ncov-tools_summaries.sh /path/to/SIGNAL/results