8. Walkthroughs

a. Tiny Example: Constructing and Modifying a Francisellaceae FlexTaxD Database

This section provides a step-by-step guide on how to build a FlexTaxD database focused on the Francisellaceae family. It includes instructions for initial database creation and subsequent modification to the tularensis branch, complemented by visual aids.

b. Building a FlexTaxD Database with GTDB Taxonomy

Here, we delve into the process of generating a FlexTaxD database using the GTDB taxonomy framework and the representative genome dataset, including optional modifications to tailor the database to specific needs.

c. Creating an NCBI-Based FlexTaxD Database

This guide covers the creation of a FlexTaxD database by leveraging NCBI taxonomy data. It includes comprehensive steps for downloading the necessary genomic data and integrating it into the database, with options for customization.

d. Merging NCBI and GTDB Databases with FlexTaxD

A thorough walkthrough describing the process of constructing individual FlexTaxD databases from NCBI and GTDB sources, followed by detailed steps to merge these databases, specifically focusing on replacing certain NCBI branches with GTDB data.

e. Creating a 16S rRNA GTDB Kraken2 Database with FlexTaxD

This tutorial explains how to use FlexTaxD to construct a Kraken2-compatible database using GTDB's 16S rRNA data, ensuring compatibility and ease of use for metagenomic classification tasks.

f. Generating a SILVA 16S rRNA Database for Kraken2 Using FlexTaxD

A step-by-step guide on creating a Kraken2 database from the SILVA 16S rRNA dataset using FlexTaxD, intended for users seeking to utilize SILVA's comprehensive rRNA databases for metagenomic analysis.