Fig. 1

Scheme of the 2bRAD-M workflow. In the library preparation module of the 2bRAD-M pipeline, DNA samples were first digested using a type IIB restriction enzyme. The resulting 2bRAD fragments were enriched and amplified for DNA sequencing. In the computational module of the 2bRAD-M pipeline, we employed both prebuilt and sample-specific 2bRAD marker database to perform taxonomic profiling on 2bRAD data. Firstly, all reads were mapped against the default prebuilt unique 2bRAD marker database (2b-Tag-DB) to identify all candidate species in a 2bRAD-M sample. Next, to accurately estimate the abundance of identified species, we increased the number of taxa-specific 2bRAD markers for each candidate species by reconstructing a reduced 2bRAD marker database (sample-specific 2b-Tag-DB) which contains more 2bRAD markers specific to each candidate species than those in the default 2b-Tag-DB. All the 2bRAD sequences were then remapped to this sample-specific 2b-Tag-DB for abundance estimation of candidate species. In principle, the relative abundance of a given species was calculated as the read coverage of all species-specific 2bRAD markers. For more information, please refer to the “Materials and Methods” section