Table 2 Percentage of reads lost at each stage of the bioinformatic pipeline and over the entire bioinformatic process, for each Illumina MiSeq run
Bacteria | Fungi | |||
|---|---|---|---|---|
Bioinformatic pipeline step | Run1 | Run2 | Run3 | Run4 |
Primers removal with Cutadapt | 11.97% | 14.04% | 5.12% | 5.07% |
Quality filtering with DADA2 | 7.53% | 4.43% | 9.47% | 10.52% |
Chimera removal | 19.01% | 19.01% | 9.3% | 5.76% |
Removal of ASVs not assigned to a microbial kingdom | 0.11% | 0.12% | 2.19% | 0% |
Decontamination (Galan's filter) | 3.27% | 5.23% | 3.97% | 3.96% |
Decontamination (Decontam filter) | 0.79% | 11.14% | 5.66% | 6.86% |
Removal of singletons and samples with less than 100 reads | 0% | 0.4% | 0% | 0% |
Total read lost | 42.68% | 54.37% | 35.71% | 32.17% |