Taxonomic Placement

Overview

Teaching: 10 min
Exercises: 10 min

Questions

• What is the taxonomic classification of my genome?

Objectives

• Assigning taxonomic classiffication to a newly assembled genomes using available tools.

Downloading the assembled sequence

We now have an assembled genome that we can analyze. Before moving forward, we would like to determine the lineage or taxonomic classification of this newly assembled genome. For that, we will need to first download the genome from galaxy.

1. Find the medaka consensus pipeline - Consensus result and click the Download icon (first from left) to save it to your computer. Hint: The file should be in .fasta format.

Taxonomic Placement with autoMLST

We will use autoMLST to get an overview which gives us the most similar organisms. Unfortunately, it is not available in the Galaxy server, so we must do the analysis in the autoMLST webserver.

1. Go to the autoMLST webserver
2. Choose the Placement (Fast) mode
3. Upload your genome sequence
4. Enter your email to get your result back
5. Click Submit job

Other tools to consider

There are also other bioinformatic tools for phylogenomic placement. Unfortunately, many of these tools are only available as a command line interface. Here are some tools to consider:

GTDB-tk

a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes by placing the sequence to the GTDB tree database.

RefSeq_Masher

Find what NCBI RefSeq genomes match or are contained within your sequence data using Mash MinHash with a Mash sketch database of 54,925 NCBI RefSeq Genomes.

Discussion 01

Solution

TBD

Key Points

• Taxonomic placement of a newly assembled genome can be achieved by calculating nearest reference organism and placing the query genome into existing tree in the database. Such example of tools are autoMLST and GTDB.