Sequence analysis
The sequence analysis was done using the OBITools package (Boyer
et al., 2016). Briefly, forward and reverse reads were assembled usingilluminapairedend program before assigning the assembled
sequences to the different samples using the ngsfilter . The
original dataset was split into several files using the obisplitprogram, one file per sample and primer pair. Sequences corresponding
most likely to PCR or sequencing errors were discarded. The discarded
sequences were shorter than 20 bp, or occurring less than 10 times per
sample, or labeled as ”internal” by the obiclean program. The
taxonomic assignment was carried out with the ecotag program,
using a curated reference database (Prié et al. 2020) or a database
extracted from the EMBL release 138. Only sequences with a similarity
higher than 98% with one of the databases were kept. All sequences with
a frequency of occurrence below 0.001 were considered as potential
tag-jumps (Schnell, Bohmann, & Gilbert, 2015) and discarded.