Hi @sstadick and thanks a lot for developing perbase!
I'd love to use perbase to estimate the final coverages of multisteps short/long/hybrid bacterial whole-genome assemblies. For these use cases, a distinct tool for per-sequence summarizing information would be very helpful.
For example if we could get the following information for each sequence within an assembly:
- seq-id
- min coverage
- average coverage
- max coverage
- normalized cov
By "normalized cov" I mean the average coverage of a seq normalized to the average coverage of the longest sequence, like in Unicycler. By this we get important information, as for example that a sequence "B" has 5x the coverage of sequence "A" (often the longest sequence is the chromosome or at least a larger part of it).
Again thanks and best regards!
Hi @sstadick and thanks a lot for developing perbase!
I'd love to use perbase to estimate the final coverages of multisteps short/long/hybrid bacterial whole-genome assemblies. For these use cases, a distinct tool for per-sequence summarizing information would be very helpful.
For example if we could get the following information for each sequence within an assembly:
By "normalized cov" I mean the average coverage of a seq normalized to the average coverage of the longest sequence, like in Unicycler. By this we get important information, as for example that a sequence "B" has 5x the coverage of sequence "A" (often the longest sequence is the chromosome or at least a larger part of it).
Again thanks and best regards!