  Metabarcoding on amplicons is rapidly expanding as a method to produce
molecular based inventories of microbial communities. Here, we work on
freshwater diatoms, which are microalgae possibly inventoried both on a
morphological and a molecular basis. We have developed an algorithm, in a
program called diagno-syst, based a the notion of informative read, which
carries out supervised clustering of reads by mapping them exactly one by one
on all reads of a well curated and taxonomically annotated reference database.
This program has been run on a HPC (and HTC) infrastructure to address
computation load. We compare optical and molecular based inventories on 10
samples from L\'eman lake, and 30 from Swedish rivers. We track all
possibilities of mismatches between both approaches, and compare the results
with standard pipelines (with heuristics) like Mothur. We find that the
comparison with optics is more accurate when using exact calculations, at the
price of a heavier computation load. It is crucial when studying the long tail
of biodiversity, which may be overestimated by pipelines or algorithms using
heuristics instead (more false positive). This work supports the analysis that
these methods will benefit from progress in, first, building an agreement
between molecular based and morphological based systematics and, second, having
as complete as possible publicly available reference databases.
