Im all in favour of adding RiboDetector or simply aligning against the contaminants list like Ira does and Svetlana mentioned. A-site tracks are definitely more valuable than coverage for Ribo-Seq. A-site should also be the target over p-site even though much of the field focuses on p-sites. The a-site is where the decoded codon sits when recognised by the tRNA and therefore interpreting P-sites would mean you would misinterpret various peaks/stalls. P-sites are relevant for initiating ribo-seq. Just for the record I certainly didn't mean to object to the inclusion of plastid just whether it was needed for that milestone at the time. Your use case is perfectly valid. It is a classic piece of Ribo-Seq software and from the lab who founded the technique. However maybe you'd like to look into RiboWaltz as well especially as its on bioconda already I would handle detection and quantification of translated regions as two different problems. Both have similar challenges and of course some detection tools will output quantification data but just because you dont de novo call a given translated region from a given dataset doesn't mean its not being translated. Rather than p-site calculations being to the end of quantification, generate A-site profiles that can be used for browser tracks and for quantification. They will however be only able to be used for quite naive quantification and only in cases where the full region was mappable. There isnt really a suitable quantification tool for Ribo-Seq that handles multimappers and overlapping translated regions properly yet. Then a separate effort should be to add more detection tools but we will need to be clear with users that the resulting calls will not be all that reliable unless coverage is very high.