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.