I am looking for a tool that can provide a high level summary of coverage statistics of genomes used in an alignment.

I concatenated GCF_000002285.5_Dog10K_Boxer_Tasha_genomic.fna, GCF_000001405.39_GRCh38.p13_genomic.fna, and GCF_000001635.27_GRCm39_genomic.fna. Each of these animal genomes contains hundreds of chromosome sequences.

I have aligned RNASeq data to this combined dog-human-mouse reference and now I would like to calculate the total number of reads, coverage of each animal genome and depth of coverage. I am only interested in animal level summary, not chromosome coverage statstics.

Tools such as mosdepth, depth-cover, qualimap (V2.2.1) only provide coverage at a chromosome level, not a summary at full genome level (eg coverage 1x, 4x, 10x depths).

>Update after a couple of days: Pehaps what I can do is get all the chromosome accessions for each of the genomes. Then extract from the .bam (forst convert to sam) result 3 seperate files containing only the results relevant to each genome. Then find a tool that will calculate summary statistics on each of the 3 sam files (total coverage at depth n, total number of reads mapped).




  [1]: https://github.com/shiquan/bamdst
  [2]: http://bamstats.sourceforge.net/
Will use [Pysam][1] to write code to do this


  [1]: https://pysam.readthedocs.io/en/latest/api.html#api