Taxonomic NCBI

Contents

• Introduction
• Guide
• Download
• Running on macOS, Linux and BSD PCs

Introduction

Taxonomic NCBI is designed to annotate a read count file with the sequence's species of origin initially using NCBI's GenBank and taxonomic data. A generic workflow is given below, but it should be noted that as Taxonomic NCBI processes plain text files, there is not set method to create the read count file or identify a sequence's origin as long as the file have a consistent format and contain the required data.

A generic workflow:

• A BLAST database is searched with blastn to identify hits for each sequence in the read count file. This database can be a NCBI genBank database or a custom database created using for example with SILVA or BOLD data.
• The Hits sequence descriptor is used to identify the species of origin.
• The NCBI Taxonomy data set is then searched using the species name to obtain the sequence's Taxonomic data.
• The data is then linked to the BLAST results file.
• The annotated BLAST results file is then combined with the read counts file to produce a reads count matrix annotated with taxonomic data.
• The annotated reads count file can then be filtered and aggregated with respect to:
  • If the species linked to a sequence is not present in the sampled habitat, but a close relative is, the species data can be switched.
  • The sequence's BLAST hit results: percent identity and or e score, etc.
  • A sequence's total read count.
  • Sequences can be flagged or filtered if the sequence's taxonomic data (i.e., species name) is present in a 2nd file.
  • Read count data can be aggregated based on whether sequences share the same taxonomic grouping i.e. same species or family name.

Taxonomic NCBI is written to be flexible and so can process sequence descriptors from a range of sources such as the SILVA data set or standard GenBank sequence description. The only requirement for automated analysis is that the the descriptions have a consist format structure.

As well as allowing the automated annotation of a file, Taxonomic NCBI will also allow you to perform manual searchers using either names (common English or Latin) or the species' NCBI taxonomy ID number.

Guide

The Taxonomic NCBI guide is here.

Download

The compiled program can be downloaded from here.

Running on macOS, Linux or BSD computers

Taxonomic NCBI can run on arrange of non-Windows PCs that have an Intel or AMD processor as described here.