iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates. We implemented the following functions in iVar: (1) trimming of primers and low-quality bases, (2) consensus calling, (3) variant calling – both iSNVs and insertions/deletions, and (4) identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.
Floki is a tool(under active development) that can be used to visualize and interpret metagenomic data using the hierarchical taxonomy structure. It can be used to identify and filter out contaminants. It can also be used to visualize batch effects by grouping multiple samples together. Annotations from other sources at every taxon level can be combined with sequencing results to narrow down the search space for taxons of interest.
An R package to access outbreak.info API. The package includes functions that allow users to easily retrieve data from the API for downstream analysis and visualization. Users can retrieve data by specifying administrative level (World Bank region, country, state/province, metropolitan area, county), location name(s), or by constructing a custom query with additional parameters. The package also allows users to directly plot metrics of interest for the specified locations. The api also includes the geometric features of each queried location allowing users to quickly create maps to visualize epidemiological data.