Software description
NGSpeciesID is a program developed in python that wraps a set of tools for read clustering, consensus forming, and consensus polishing (Figure 1). It is a one-software solution and extension of the Saiga pipeline, we developed previously (Seah et al., 2020). It can be easily installed using the free and open-source Anaconda distribution. Briefly, NGSpeciesID clusters amplicon sequencing reads (in fastq format) and forms a consensus sequence for each cluster. Next, it merges reverse complement clusters. Finally, the remaining consensus sequence(s) is/are polished. Optionally, the tool can also remove primer sequences from the consensus after the polishing step. In the following sections we describe the workflow of NGSpeciesID, which is freely available athttps://github.com/ksahlin/NGSpeciesID . For more details see Supplementary File 1 and Figure 1.