Has anyone ever tried to generate base qualities for a next-gen genome assembly using a .bam alignment of the short reads back to that assembly? I imagine that regions with lower mapq scores could be marked as less confident for example. Also regions where many reads disagree with the base calls at a certain position can be downrated on quality. Additionally the base qualities of all of the reads that align in a certain column might be usable to help assign a genome base quality to that column. Does anyone know of a tool that does this? I tried doing a quick google search and haven't come up with anything that sounds promising yet. I am using Allpaths-lg which doesn't appear to output any kind of base quality statistics for the assembly. NCBI recommends submitting assemblies with base-quality statistics (although it is not required). Basically I am willing to try a bit to generate this kind of file as it may be usable for some downstream analysis (none that I am doing though), but I am going to stop short of writing my own software to do it.
