strollur accepts two formats for classification data: full or tidy.
Details
The full taxonomy table is a data.frame with two columns: sequence_name
or bin_name, and taxonomy. The taxonomy column contains the full
classification string.
The full taxonomy table format:
sequence_name
M00967_43_000000000-A3JHG_1_1102_26308_14496
M00967_43_000000000-A3JHG_1_1103_22654_26891
taxonomy
Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);
Bacteria(100);Firmicutes(99);Clostridia(99);Clostridiales(99);The tidy taxonomy table is a data.frame with 4 columns: sequence_name
or bin_name, taxonomy, level, and confidence. For example:
The tidy taxonomy table format:
sequence_name taxonomy
M00967_43_000000000-A3JHG_1_1102_26308_14496 Bacteria
M00967_43_000000000-A3JHG_1_1102_26308_14496 "Bacteroidetes"
M00967_43_000000000-A3JHG_1_1102_26308_14496 "Bacteroidia"
M00967_43_000000000-A3JHG_1_1102_26308_14496 "Bacteroidales"
M00967_43_000000000-A3JHG_1_1103_22654_26891 Bacteria
M00967_43_000000000-A3JHG_1_1103_22654_26891 Firmicutes
M00967_43_000000000-A3JHG_1_1103_22654_26891 Clostridia
M00967_43_000000000-A3JHG_1_1103_22654_26891 Clostridiales
level confidence
1 100
2 100
3 100
4 100
1 100
2 99
3 99
4 99