Programme Parameters
Foundation
3 Days (4.5 Hrs)
Online (e-LMS)
• No prior experience required — basic computer literacy is sufficient.
• A laptop or desktop with a stable internet connection.
• Willingness to complete assignments and the capstone project.
About This Course
This Hands-On AMR Course teaches a practical, in-demand bioinformatics skill: finding antimicrobial-resistance genes in genomic data. You learn how sequence-similarity search with BLAST works, how to query genomic and assembly data against curated resistance databases such as CARD and ResFinder, and how to interpret the hits — distinguishing true resistance determinants from noise. Grounded in the global public-health urgency of AMR surveillance, the course walks from raw sequence to a defensible resistance profile. You finish able to run and interpret an AMR gene-detection workflow. A verified e-Certificate of competency and e-Marksheet from the Deep Science & Technology Consortium.
🎯 Program Aim
This hands-on course teaches detection of antimicrobial-resistance (AMR) genes from genomic data using BLAST and resistance databases, from sequence to interpretation.
📋 Course Objectives
1. Explain sequence-similarity search with BLAST.
2. Query genomic data against CARD and ResFinder.
3. Detect and annotate resistance genes.
4. Distinguish true determinants from spurious hits.
5. Produce a defensible resistance profile.
👥 Who Should Enroll?
• Microbiology and genomics researchers
• Bioinformatics and public-health professionals
• AMR-surveillance and clinical-lab staff
• Students specialising in bioinformatics
🚀 Key Learning Outcomes
• The ability to detect AMR genes from sequence data.
• A hands-on AMR bioinformatics workflow.
• A skill directly relevant to AMR surveillance.
• A verified e-Certificate of competency and e-Marksheet from the Deep Science & Technology Consortium.
💎 What You'll Gain
Live & Recorded Sessions
Lifetime access to class recordingse-Certificate on Completion
Cryptographically verified credentialPost-Programme Support
Direct access to mentors & councilHands-On Experience
Notebooks, real-world code & datasetsCurriculum Outline
Navigating NCBI
• GenBank, RefSeq, SRA and BioSample, and what each record actually guarantees
• Retrieving sequences and metadata programmatically with E-utilities
• Record quality: annotation errors and misidentified submissions
Similarity Search Done Correctly
• BLAST flavours and choosing between blastn, blastp and tblastn
• E-value, bit score, identity and coverage, and why identity alone misleads
• Building and searching a local database for reproducible results
Dedicated Resistance Resources
• CARD, ResFinder and AMRFinderPlus, and their differing curation philosophies
• Acquired resistance genes versus chromosomal resistance mutations
• Thresholds for calling a gene present, and disagreement between tools
Genotype to Phenotype
• Why a detected gene does not guarantee expressed resistance
• Correlating predictions with phenotypic susceptibility testing
• Mobile genetic elements, plasmids and transmissibility
Reproducible Analysis
• Scripting the workflow so a result can be regenerated
• Version pinning of databases, which change underneath you
• Reporting conventions for surveillance and publication
Technical Specifications
| Parameter | Requirement |
|---|---|
| Covered Tool / Platform | Python |
| Covered Tool / Platform | R/Bioconductor |
| Covered Tool / Platform | BLAST |
| Covered Tool / Platform | Biopython |
| Covered Tool / Platform | Galaxy |
| Covered Tool / Platform | UniProt |
| Covered Tool / Platform | NCBI |
| Covered Tool / Platform | PyMOL |
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