Small python script to compute coverage of contigs from reads. compute_coverage uses minimap2 to map the reads to the assembly and deduces the coverage of each contig.
usage: compute_coverage.py [-h] -i INPUT -r READS -o OUTPUT [-t THREADS]
[-x PRESET] [--minimap2 MINIMAP2]
Add depth information to an assembly
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Input assembly (fasta or gfa)
-r READS, --reads READS
Reads used to generate the assembly (fasta or fastq,
can be gzipped)
-o OUTPUT, --output OUTPUT
Output assembly (same format as input)
-t THREADS, --threads THREADS
Number of threads to use [1]
-x PRESET, --preset PRESET
Minimap2 preset to use [map-ont]
--minimap2 MINIMAP2 path to minimap2 executable [minimap2]