Use cases and comparison to other tools
We tested our software on publicly available data from Maestri et al. (2019) and Wurzbacher et al. (2019), and compared the accuracy of respective consensus sequences generated in the two studies to those reconstructed with NGSpeciesID. To measure accuracy, we aligned the consensus sequences to the Sanger sequence using BLAST (Altschul et al., 1990) and calculated accuracy as the sum of all matches in the alignment divided by the alignment length. We chose the software solution presented in Wurzbacher et al., (2019) for our comparison as it is currently, to our knowledge, the only one that can handle both PacBio and ONT sequencing reads. We further compared our result to the ONTrack software (Maestri et al., 2019) developed for ONT data specifically. In both comparisons we carried out polishing within NGSpeciesID using Medaka (https://github.com/nanoporetech/Medaka) and Racon (Vaser et al., 2017).