Report aligned bases

[Shians]

Would it be possible to report % aligned bases on top of % aligned reads?

[wdecoster]

Not easily, in the current implementation, or not without a lot of overhead. The closest you can currently get is to run with default settings on your aligned bam, and once with --ubam on an unaligned bam. But I agree that is not great. Could you elaborate on why that would be an important metric for you?

Thanks,
Wouter

[Shians]

I consider the amount of throughput of a long-read experiment to be the gigabases sequenced rather than number of reads. By extension I think of the proportion of gigabases aligned to be the measure of useful data obtained.