Additional file 6 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis
Additional file 6 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis
Additional file 6: Supplementary Figure S2. Reproducibility and data usage efficiency respective to dereplication filtering. A, D and G) Data usage efficiency of each tested pipeline at different dereplication parameters of LotuS2 (from strictest to least strict dereplication: 20:1,12:3,6:2; 15:1,9:3,12:2; 10:1,6:3,8:2; 8:1,4:2,3:3 (default); 4:1; 2:1, and 1:1) using DADA2 or CD-HIT clustering for 16S and ITS datasets, respectively, by comparing the number of sequence clusters (OTUs/ASVs) to retrieved read counts in final output matrix.The dereplication can be fine controlled through a syntax. For example, 8:1,4:2,3:3 means that a read is accepted, if it occurs >=8 times in >= 1 samples or >4 times total in >= 2 samples or >=3 times in >= 3 samples.
- University of Tartu Estonia
- Swedish University of Agricultural Sciences Sweden
- Quadram Institute United Kingdom
- Earlham Institute United Kingdom
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