BamToCov is a suite of tools for coverage analysis written in Nim and built upon the memory efficient algorithm of covtobed.
We designed BamToCov to fill some gaps in coverage analysis:
- Accepting input streams (i.e. not requiring the BAM index, at the expense of speed)
- Enabling per strand coverage analysis
- Enabling the physical coverage analysis
- Using a minimum amount of memory (minimum memory usage)
This makes BamToCov a useful companion especially when testing pipelines on small datasets.
For coverage analysis of large datasets it can be useful to consider Mosdepth, that uses indexed BAM/CRAM files as input. Another interesting alternative is Megadepth, a fast and memory efficient tool.