Matt

i'd also be interested in this - what is the threshold for reporting values? it's described as 'much below 80%' in the readme but that isn't particularly helpful as some...

sure - looks like this is the one i used (written hastily a long time ago so not my best work!) [sort_json.py.zip](https://github.com/rjchallis/assembly-stats/files/12289282/sort_json.py.zip)

just to add to this - I had a similar issue that was solved by using simple sequence ids (e.g. seqkit seq --only-id)

might be reproducing taxonkit profile2cami? https://bioinf.shenwei.me/taxonkit/usage/#profile2cami

so you're pretty much already there with the standard taxpasta output. but instead of the two columns (taxid & count) you'd need to provide taxid & abundance (i.e. percentage) and...

I think maybe they are talking about proportion vs percentage and not counts but not totally sure

Maybe don’t do away with counts altogether though? I actually find it more useful to have them instead because you can’t convert backwards to counts from abundances. An additional output...