6.2 Activity - Kickstart Project Work

6.2.1 Learning Objectives

1. Import an example SRA sequencing data file by accession id (e.g. SRR)
2. Perform classification of nanopore-sequenced soil MAGs with GTDB-Tk
3. Import an SRA dataset you would like to analyze for your research project
4. Use a new Galaxy tool that we have not worked through in class

6.2.2 Activity 1 - Import an SRA file into Galaxy

6.2.2.1 Instructions

1. Upload sequencing reads for accession id SRR29980924 in Galaxy using Faster Download and Extract Reads in FASTQ tool .
2. Make your Galaxy history sharable.

6.2.2.2 Questions

1. Share your Galaxy history with SRR29980924fastq data you downloaded with Faster Download and Extract Reads in FASTQ tool.
Galaxy history Link:

2. Find and record the following features of your downloaded dataset below.
File size:
File format:
Job Runtime (Wall Clock):
First line of the sequencing file:

3. Inspect SRR29980924 entry in NCBI https://www.ncbi.nlm.nih.gov/sra. Obtain the following sequencing information.
Organism:
Instrument:
Strategy:
Run:

6.2.3 Activity 2 – Taxonomically classify nanopore-soil-subset MAGs with GTDB-Tk in Galaxy

6.2.3.1 Instructions

Using GTDB-Tk Classify genomes tool, classify the nanopore-soil MAGs you obtained from MetaBAT2 binning of contigs during Project: Finding AMRs, Activity 4. Note, MetaBAT2 bins are a collection, so try using Dataset collection (instead of multiple individual files) as input.

6.2.3.2 Questions

1. Record summary of MAG classification of Bacteria below.

2. Record summary of MAG classification of Archaea below.

3. Share your Galaxy history to GTDBtk classification below.

6.2.4 Activity 3 – Import an SRA dataset of interest for your research project

6.2.4.1 Instructions

Upload sequencing reads from a dataset of interest using the Faster Download and Extract Reads in FASTQ tool. Refer back to the table in the Activity: Possible Datasets for BioProjects with known long read metagenomics datasets.

6.2.4.2 Questions

1. Record the following features of your downloaded dataset below.
Accession ID:
File size:
Job Runtime (Wall Clock):

2. Inspect your SRA entry in NCBI https://www.ncbi.nlm.nih.gov/sra. Obtain the following sequencing information.
Organism:
Instrument:
Strategy:
Run:

6.2.5 Activity 4 – Use a new Galaxy tool that may be useful for your project

6.2.5.1 Instructions

Find one new Galaxy tool that you think may be useful for your research project. A few possibilities to get you started include:

• Prokka Galaxy tutorial
• Bakta Galaxy Tutorial
• antiSMASH [Galaxy tutorial](http://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html
• CheckM2 Galaxy tutorial
• Tools mentioned in tutorials like GTN: Bacterial Genome Annotation
• Tools used in workflows like https://nf-co.re/mag (not all tools will be available on Galaxy)

6.2.5.2 Questions

1. Briefly describe the tool e.g. how it works, what it takes as input, and what it produces as output.

2. Describe briefly any problems you had running the tool and troubleshooting steps you tried.

3. If you were able to get the tool to run, describe the results and whether they provide additional information for your project.

6.2.6 Grading Criteria

• Download as Microsoft Word (.docx) and upload on Canvas

6.2.7 Footnotes

Resources

• Google Doc

Contributions and Affiliations

• Valeriya Gaysinskaya, Johns Hopkins University
• Frederick Tan, Johns Hopkins University

Last Revised: June, 2025

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All materials CC-BY unless noted otherwise.