Bioinformatics and NGS Sequence Analysis Task Portal 01
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Bioinformatics and NGS Sequence Analysis – Program Update
The Bioinformatics and NGS Sequence Analysis Internship is designed to help students develop practical skills in bioinformatics, genomic data analysis, and next-generation sequencing (NGS) technologies. The program combines biological sciences, computational methods, programming, and data analysis to help participants understand and analyze real-world sequencing datasets.
Throughout the internship, participants will:
- Learn the fundamentals of bioinformatics and computational biology
- Understand DNA, RNA, genes, genomes, and biological sequence data
- Learn the fundamentals of Next-Generation Sequencing (NGS)
- Explore NGS workflows and sequencing data analysis
- Perform DNA and RNA sequence analysis using bioinformatics tools
- Understand sequence quality assessment and preprocessing
- Study genome and transcriptome analysis concepts
- Learn basic sequence alignment and biological database searching
- Gain hands-on experience with genomic and biological datasets
- Analyze NGS data through practical exercises and research-based case studies
- Build a mini-project based on bioinformatics and NGS sequence analysis
Each Task Includes:
- 🧑💻 Session-based learning
- 📝 Bioinformatics notes and preparation
- 🧬 DNA/RNA sequence analysis exercises
- 📊 NGS data analysis and interpretation
- 💻 Practical computational assignments
- 🧪 Research-based genomic case studies
- 📤 Submission via Google Forms
By the end of the internship, students will gain practical exposure to bioinformatics, NGS technologies, genomic data analysis, sequence analysis, biological databases, and computational approaches used in modern genomics and biotechnology research.
TASK 1: Introduction to Analysis of Next-Generation Sequencing Data
🎯 Objective:
Understand the fundamentals of Next-Generation Sequencing (NGS), NGS data analysis workflow, and the importance of computational methods in modern genomics and bioinformatics.
🧩 Session:
Session 01 – Introduction to Analysis of Next-Generation Sequencing Data
Session Link: https://drive.google.com/file/d/1d4ANiMKuSn89O57j7v3ay_IXYBnTK4y0/view?usp=sharing
📝 Task:
Write Notes On:
- What is Next-Generation Sequencing (NGS)?
- Difference between Sanger sequencing and NGS.
- Major applications of NGS.
- Types of NGS sequencing technologies.
- Basic NGS data analysis workflow.
- Importance of bioinformatics in NGS data analysis.
- Common file formats used in NGS analysis.
🔬 Practice / Research:
- Research 3 real-world applications of NGS.
- Identify 3 commonly used NGS platforms.
- Draw or explain the basic NGS data analysis workflow.
- Research how NGS is used in disease diagnosis or genomic research.
📚 Assignment:
Write a short report (200–300 words):
“How Next-Generation Sequencing is Transforming Modern Genomics and Healthcare.”
📂 Internship Task Completion Status
After completing this task, interns must fill out the Internship Task Completion Status Form and upload:
- Session Notes
- Assignment Report
- Research Work (if applicable)
- Screenshots of Practical Work (if applicable)
This submission will be used to verify task completion and monitor internship progress.
🔗 Form Link: https://forms.gle/vGJe2BQzQYFiikH26
TASK 2: Install Ubuntu on a Windows Machine Using VirtualBox
🎯 Objective:
Learn how to install and configure Ubuntu Linux on a Windows computer using VirtualBox and understand the importance of Linux environments in bioinformatics and NGS data analysis.
🧩 Session:
Session 02 – Install Ubuntu on a Windows Machine (VM VirtualBox) for Sequence Analysis
Session Link: https://drive.google.com/file/d/1rAVziMcOcwpoG0hWf-CHQYIb4f8uegO7/view?usp=sharing
📝 Task:
Write Notes On:
- What is Ubuntu?
- What is Linux and why is it used in bioinformatics?
- What is VirtualBox?
- What is a Virtual Machine (VM)?
- Steps involved in installing Ubuntu using VirtualBox.
- Basic Ubuntu terminal commands.
- Importance of Linux in NGS data analysis.
💻 Practice / Research:
- Install Ubuntu using VirtualBox.
- Open the Ubuntu terminal and practice basic commands.
- Practice commands such as
pwd,ls,cd,mkdir,cp,mv, andrm. - Create a folder structure for storing NGS data.
- Research why most bioinformatics tools are developed for Linux environments.
📚 Assignment:
Write a short report (200–300 words):
“Why Linux and Ubuntu are Widely Used in Bioinformatics and NGS Data Analysis.”
📂 Internship Task Completion Status
After completing this task, interns must fill out the Internship Task Completion Status Form and upload:
- Session Notes
- Assignment Report
- Ubuntu Installation Screenshot
- Terminal Practice Screenshots
- Research Work (if applicable)
This submission will be used to verify task completion and monitor internship progress.
🔗 Form Link: https://forms.gle/vGJe2BQzQYFiikH26
TASK 3: FASTQ Format and Downloading Sequence Data from NCBI SRA
🎯 Objective:
Understand the FASTQ file format and learn how to obtain publicly available sequencing datasets from the NCBI Sequence Read Archive (SRA).
🧩 Session:
Session 03 – What is the FASTQ Format? Download Files from NCBI’s SRA
Session Link: https://drive.google.com/file/d/1kQMojTYWuqakYs6GWq7iOhONttXGiaMi/view?usp=sharing
📝 Task:
Write Notes On:
- What is a FASTQ file?
- Structure of a FASTQ file.
- FASTQ sequence and quality information.
- Phred quality scores.
- Difference between FASTA and FASTQ formats.
- What is NCBI SRA?
- How to search for sequencing datasets in SRA.
- Importance of publicly available sequencing datasets.
🔬 Practice / Research:
- Visit the NCBI SRA database.
- Search for an NGS dataset of your choice.
- Identify the accession number of the dataset.
- Download a sequencing dataset.
- Open the FASTQ file and identify its four-line structure.
- Research the meaning of sequencing quality scores.
📚 Assignment:
Write a short report (200–300 words):
“Understanding FASTQ Files and Their Importance in NGS Data Analysis.”
📂 Internship Task Completion Status
After completing this task, interns must fill out the Internship Task Completion Status Form and upload:
- Session Notes
- Assignment Report
- SRA Dataset Accession Number
- Downloaded Dataset Screenshot
- FASTQ File Screenshot
- Research Work (if applicable)
This submission will be used to verify task completion and monitor internship progress.
🔗 Form Link: https://forms.gle/vGJe2BQzQYFiikH26
TASK 4.1: Check Sequencing Reads for Quality Using FastQC
🎯 Objective:
Learn how to evaluate the quality of raw sequencing reads using FastQC and identify common quality issues in NGS datasets.
🧩 Session:
Session 04.1 – Check Your Sequenced Reads for Quality Using FastQC
Session Link: https://drive.google.com/file/d/1vI50L4ukukOp8XOPSNUs0FBpN9uis-p1/view?usp=sharing
📝 Task:
Write Notes On:
- What is sequencing quality control?
- What is FastQC?
- Why is quality checking important before NGS analysis?
- How to install FastQC.
- How to run FastQC on FASTQ files.
- Important FastQC reports and modules.
- Sequence quality scores.
- Per-base sequence quality.
- Adapter content and sequence duplication.
🔬 Practice / Research:
- Install FastQC in the Ubuntu environment.
- Run FastQC on a downloaded FASTQ dataset.
- Generate a FastQC report.
- Examine the different quality-control modules.
- Identify whether the sequencing reads have any quality issues.
- Take screenshots of the generated FastQC report.
📚 Assignment:
Write a short report (200–300 words):
“Importance of Quality Control in Next-Generation Sequencing Data Analysis.”
📂 Internship Task Completion Status
After completing this task, interns must fill out the Internship Task Completion Status Form and upload:
- Session Notes
- Assignment Report
- FastQC Installation Screenshot
- FastQC Report
- Quality Analysis Screenshots
- Research Work (if applicable)
This submission will be used to verify task completion and monitor internship progress.
🔗 Form Link: https://forms.gle/vGJe2BQzQYFiikH26
TASK 4.2: Interpretation of FastQC Results
🎯 Objective:
Learn how to interpret FastQC reports and identify sequencing-quality problems that may affect downstream bioinformatics analysis.
🧩 Session:
Session 04.2 – Check Your Sequenced Reads for Quality and Interpret FastQC Results
Session Link: https://drive.google.com/file/d/18yO8nn6llL4030kTX3IWQQaQF7I3Wo3J/view?usp=sharing
📝 Task:
Write Notes On:
- Understanding the FastQC report.
- Per-base sequence quality.
- Per-sequence quality scores.
- Sequence length distribution.
- GC content.
- Sequence duplication levels.
- Overrepresented sequences.
- Adapter contamination.
- PASS, WARN, and FAIL indicators.
- Importance of FastQC results in preprocessing.
🔬 Practice / Research:
- Analyze a FastQC report generated from an NGS dataset.
- Identify modules marked PASS, WARN, and FAIL.
- Identify possible adapter contamination.
- Examine GC-content distribution.
- Identify any unusual sequencing patterns.
- Prepare a brief quality assessment of the dataset.
📚 Assignment:
Write a short report (200–300 words):
“How FastQC Helps Identify Quality Issues in NGS Data.”
📂 Internship Task Completion Status
After completing this task, interns must fill out the Internship Task Completion Status Form and upload:
- Session Notes
- Assignment Report
- FastQC Report
- Quality Interpretation
- Screenshots of Important FastQC Modules
- Research Work (if applicable)
This submission will be used to verify task completion and monitor internship progress.
🔗 Form Link: https://forms.gle/vGJe2BQzQYFiikH26
TASK 5: Install EA-Utils for Processing Sequence Reads
🎯 Objective:
Learn how to install and use EA-Utils for processing sequencing reads, including quality trimming and removal of unwanted sequences such as adapters.
🧩 Session:
Session 05 – Install EA-Utils to Process Sequence Reads
Session Link: https://drive.google.com/file/d/10q1A-buw-RDHvpA1emXnzP3DMULMpDra/view?usp=sharing
📝 Task:
Write Notes On:
- What is sequence preprocessing?
- Why is preprocessing important in NGS analysis?
- What is EA-Utils?
- Tools available in EA-Utils.
- Quality trimming of sequencing reads.
- Adapter removal.
- Importance of removing low-quality bases.
- Difference between raw and processed sequencing reads.
🔬 Practice / Research:
- Install EA-Utils in Ubuntu.
- Identify the appropriate tool for processing FASTQ reads.
- Perform quality trimming on sample sequencing data.
- Remove adapter sequences where applicable.
- Compare raw and processed reads.
- Run FastQC again after preprocessing and compare the results.
📚 Assignment:
Write a short report (200–300 words):
“Importance of Quality Trimming and Adapter Removal in NGS Data Processing.”
📂 Internship Task Completion Status
After completing this task, interns must fill out the Internship Task Completion Status Form and upload:
- Session Notes
- Assignment Report
- Installation Screenshot
- Commands Used for Processing
- Before-and-After Quality Reports
- Practical Work Screenshots
This submission will be used to verify task completion and monitor internship progress.
🔗 Form Link: https://forms.gle/vGJe2BQzQYFiikH26
TASK 6: Understanding Sequence Alignment
🎯 Objective:
Understand the concept of sequence alignment, its importance in bioinformatics, and how sequencing reads are compared with reference sequences.
🧩 Session:
Session 06 – What is Sequence Alignment?
Session Link: https://drive.google.com/file/d/1v87yNCOznwGLOmjkM-kSZEvrNPoO7IJK/view?usp=sharing
📝 Task:
Write Notes On:
- What is sequence alignment?
- Why is sequence alignment important?
- Pairwise sequence alignment.
- Multiple sequence alignment.
- Global vs local alignment.
- Reference genome.
- Read mapping.
- Alignment scores.
- Match, mismatch, and gap.
- Applications of sequence alignment in genomics.
🔬 Practice / Research:
- Research the difference between global and local alignment.
- Identify commonly used sequence alignment tools.
- Study the basic process of mapping NGS reads to a reference genome.
- Explore how alignment is used for variant identification.
- Draw a simple diagram explaining read alignment against a reference sequence.
📚 Assignment:
Write a short report (200–300 words):
“Role of Sequence Alignment in Modern Genomic Data Analysis.”
📂 Internship Task Completion Status
After completing this task, interns must fill out the Internship Task Completion Status Form and upload:
- Session Notes
- Assignment Report
- Sequence Alignment Diagram
- Research Work
- Practical Screenshots (if applicable)
This submission will be used to verify task completion and monitor internship progress.
🔗 Form Link: https://forms.gle/vGJe2BQzQYFiikH26
TASK 7.1: Align Immunome Data with IMGT – Part 1
🎯 Objective:
Understand the basics of immunome data analysis and learn how immune-related sequencing data can be aligned and analyzed using IMGT resources.
🧩 Session:
Session 07.1 – How to Align Immunome Data with IMGT (Part 1)
Session Link: https://drive.google.com/file/d/1r7Hn9mD63mnbE3fy2QOfBxbpxQ5bM9yO/view?usp=sharing
📝 Task:
Write Notes On:
- What is immunome sequencing?
- What are immune receptors?
- Introduction to antibody and T-cell receptor sequences.
- What is IMGT?
- Importance of IMGT in immunoinformatics.
- IMGT reference databases.
- Sequence alignment in immunome analysis.
- Basic workflow for immunome data analysis.
🔬 Practice / Research:
- Explore the IMGT website and available resources.
- Research the role of IMGT in immunoinformatics.
- Identify the major types of immune receptor sequences.
- Study how immunome sequencing data is analyzed.
- Prepare a basic workflow for immunome data alignment.
📚 Assignment:
Write a short report (200–300 words):
“Role of IMGT in Immunome and Immune Receptor Sequence Analysis.”
📂 Internship Task Completion Status
After completing this task, interns must fill out the Internship Task Completion Status Form and upload:
- Session Notes
- Assignment Report
- IMGT Research Work
- Immunome Analysis Workflow
- Practical Screenshots (if applicable)
This submission will be used to verify task completion and monitor internship progress.
🔗 Form Link: https://forms.gle/vGJe2BQzQYFiikH26
TASK 7.2: How to Align Immunome Data with IMGT – Part 2
🎯 Objective:
Learn how to perform and interpret immunome sequence alignment using IMGT tools, identify the closest V, D, and J gene/allele sequences, and understand the alignment results generated for immunoglobulin (IG) and T-cell receptor (TR) sequences. IMGT/V-QUEST compares input IG/TR sequences with IMGT reference sequences and provides alignment, identity, and junction information.
🧩 Session:
Session 07.2 – How to Align Immunome Data with IMGT (Part 2)
Session Link: https://drive.google.com/file/d/1EodHtnLZKKpr_MGBs4ZJTSgtZbSnfqwN/view?usp=sharing
📝 Task:
Write Notes On:
- How to submit immunome sequences to IMGT/V-QUEST.
- FASTA and FASTQ formats accepted by IMGT/V-QUEST.
- Selection of the appropriate IG or TR molecule/locus.
- Alignment of sequences with IMGT reference genes.
- V-GENE, D-GENE, and J-GENE identification.
- Understanding alignment scores and percentage identity.
- IMGT unique numbering system.
- Framework Regions (FR-IMGT) and Complementarity Determining Regions (CDR-IMGT).
- Understanding the sequence junction and its nucleotide/amino-acid representation.
- Importance of alignment results in immunome analysis.
🔬 Practice / Research:
- Open the IMGT/V-QUEST analysis tool.
- Select the appropriate receptor type and locus for the provided immunome dataset.
- Upload or enter the provided sequence data.
- Perform sequence analysis using IMGT/V-QUEST.
- Identify the closest V-GENE and allele.
- Examine D-GENE and J-GENE alignment results where applicable.
- Record the percentage of nucleotide identity and alignment score.
- Examine the FR-IMGT and CDR-IMGT regions.
- Review the junction sequence and its nucleotide and amino-acid representation.
- Take screenshots of the important analysis results.
📚 Assignment:
Write a short report (200–300 words):
“Analysis and Interpretation of Immunome Sequence Alignment Using IMGT/V-QUEST.”
📂 Internship Task Completion Status
After completing this task, interns must fill out the Internship Task Completion Status Form and upload:
- Session Notes
- Assignment Report
- IMGT/V-QUEST Analysis Screenshot
- V-GENE/D-GENE/J-GENE Identification Results
- Alignment Score and Percentage Identity
- FR-IMGT and CDR-IMGT Analysis
- Junction Analysis
- Research Work (if applicable)
This submission will be used to verify task completion and monitor internship progress.
🔗 Form Link: https://forms.gle/vGJe2BQzQYFiikH26
⏱ Estimated completion time: 5 working days per portal.