Hi all! Is there a good tool or file format for working with short read genome coverage data? We have compressed bed files and bigwig files, but is the field moving to other formats? We have been trying out the d4 format, which is great for computing things, such as gene coverage etc. on the fly on the output file. However we had some stability issues in the output, and the main tool is not actively developed. Before we decide to try and maintain that tool, is there any format do you recommend and/or are working with?

I have used TDF in the past (mostly as a compact alternative to BAMs for sharing coverage data), but they recommend bigWig due to its wider adoption and popularity. If you want to share the coverage files or store them for a long time (i.e. share with future you), I think popularity of a format, i.e. wide availability of tools that can use it, should be a consideration. If this is for non-archival internal use, pick the format that is easiest to work with for your specific application.