Input data

• genomic FASTA file
  • nucleotide sequence of your assembly divided in contigs/scaffolds
• GFF3 file
• proteins FASTA file (optional)
  • protein sequences for all protein coding genes in your data set
  • will be extracted within taXaminer pipeline using the tool gffread if not provided
• coverage information (optional, but recommended)
  • taXaminer can run with or without coverage information
  • if you wish to include it, you need one of the following:
    1. per base coverage (PBC) file: tab-separated file with 3 columns (scaffold name, base number and coverage at given position) \
    2. mapping file (BAM format): sorted and indexed \
    3. raw read FASTA files: forward and backward or unpaired raw read files
  • multiple coverage data can be used
• config file
  • YAML format