Calculate coverage (sequencing depth) of assembled genome

usually a statistical parameter in Microbiology Resource Announcements publications

General formula

Coverage (sequencing depth) = Total bases Sequenced / Size of assembled or reference genome

options:
  -h, --help            show this help message and exit
  -r REF_SIZE, --ref_size REF_SIZE
                        Size of the assembly
  --illumina_dir ILLUMINA_DIR
                        Directory containing Illumina reads in FASTQ.gz format
  --nanopore_dir NANOPORE_DIR
                        Directory containing ONT reads in FASTQ.gz format
  --platform {illumina,nanopore,hybrid}
                        Sequencing platform

example usage:

HYBRID

python coverage_calculator.py -r 4411532 --platform hybrid --nanopore_dir ~/nanopore_reads --illumina_dir ~/illumina_reads

ILLUMINA

python coverage_calculator.py -r 4411532 --platform illumina --illumina_dir ~/illumina_reads

NANOPORE

python coverage_calculator.py -r 4411532 --platform nanopore --nanopore_dir ~/nanopore_reads

Output will be saved in your current directory