Targeted metagenomics

Slots

Our working Time is 9:00 AM to 6:00 PM Indian Time Available slots - 9:00 AM to 11:00 AM / 11:00 AM to 1:00 PM / 2:00 PM to 4:00 PM / 4:00 PM to 6:00 PM
For training slots after 6 PM or before 9 am as well as weekends training kindly mention during registration accordingly it will be scheduled.

Mode

👉 For online training candidate have to install ZOOM (with remote control on candidate system which makes 100% interactive)
👉 Run time video recording candidate can make as well as pdf manual will be provided for future reference.
👉 All our training is 100% practical and 100% industrial and 100% interactive which provides same as offline learning.
👉 For doubt clear there will be extra support will be provided based on the requirement.
👉 Certificate will be provided

📘 Introduction to Bioinformatics
- Overview of bioinformatics and its applications
- Key concepts in computational biology
- Role of bioinformatics in genomics, transcriptomics, and proteomics

📘 Understanding NGS and Genomics Bioinformatics
- Basics of Next-Generation Sequencing (NGS)
- Types of NGS data (RNA-seq, WGS, WES)
- Overview of NGS data formats: FASTQ, BAM, VCF
- Introduction to pipelines and tools for NGS data analysis

📘 Databases & Data Retrieval (NCBI and UCSC)
- Learning how to retrieve biologically correct data
- Performing complete batch retrieval (e.g., whole exome)
- NCBI: understanding gene-level data retrieval
- UCSC: handling large-scale data retrieval
- UCSC Genome Browser and Table Browser usage
- Batch Coordinate Retrieval and Genomic Data downloads
- GFF/GTF gene annotation formats and how to retrieve them
- Using BLAT for sequence-based search and alignment

📘 Gene Prediction and Functional Annotation
- Gene prediction approaches and tools
- Functional annotation using Gene Ontology (GO)
- Pathway analysis using KEGG, Reactome
- Interpreting gene sets and biological relevance

📘 Standalone/Offline BLAST for Large-Scale Genomic Data
- Installing and setting up standalone BLAST
- Running local BLAST for batch sequence alignment
- Applications in genome-wide homology searches
- Custom BLAST databases and performance optimization

📘 PCR Primer Designing and Specificity Check
- Designing accurate primers for PCR amplification
- Tools: Primer3, NCBI Primer-BLAST
- Checking primer specificity using genome-wide BLAST
- Avoiding non-target amplification through design best practices

📘 Understanding Python Programming
- Introduction to Python for bioinformatics
- Scripting basics: variables, loops, functions
- Libraries like Biopython, pandas for biological data handling
- Automating genomic workflows with Python scripts

📘 Introduction to NGS Targeted Metagenome
- Understanding NGS and Its Applications
- Types of sequencing data generated
- Understanding FASTQ files and sequencing quality scores

📘 Linux Basics & Environment Setup
- Linux Command Line Basics
- Installing Targeted Metagenome Tools
- Using Conda and Shell Scripting

📘 Data Retrieval & Formats
- Fetching data from NCBI SRA using SRA Toolkit
- Understanding different file formats

📘 Introduction to R/Bioconductor
- Installing packages with CRAN and Bioconductor
- Data types and standardized data container
- Data manupulation

📘 Import Raw Data
- Load FASTQ files and sample metadata preparation for analysis

📘 Demultiplexing
- Separate pooled sequences into individual samples using barcode information

📘 Quality Control and Denoising
- Remove low-quality reads and correct sequencing errors

📘 Generate Feature Table and Representative Sequences
- Create a table showing how many times each unique sequence appears per sample, and select representative sequences for downstream steps

📘 Assign Taxonomy
- Use reference databases (e.g., SILVA, Greengenes etc) to identify the microbial taxa represented by each sequence
- Detection 16s/18s/ITS anyone candidate can select

📘 Visualize Taxonomy
- Create bar plots and summaries to show the composition and abundance of microbial taxa across your samples

📘 Phylogenetic Tree Construction
- Build a tree to understand evolutionary relationships between detected microbes; needed for phylogenetic diversity analysis

📘 Diversity Analysis
- Alpha diversity: Measures species richness and evenness within individual samples
- Beta diversity: Compares community differences between samples or groups

📘 Visualize Diversity Results
- Generate interactive plots (e.g., PCoA, Rarefaction, Krona etc) to explore patterns in microbial community structure

Preparation

- Targeted metagenomics : https://en.wikipedia.org/wiki/Metagenomics
- NCBI : https://pmc.ncbi.nlm.nih.gov/articles/PMC4585196/

Instructor

Industry Experienced

Target Audiance

This course is designed for graduate students, postdoctoral researchers, and professionals working in the fields of conservation biology, evolutionary genomics, and population genetics or any life sciences who are interested in applying genomic tools to real-world conservation challenges.

Contact

Please write us at info@arraygen.com or call or whatsapp us on mobile +91-9673625446 if you need any clarification or for any custom training based on candidate reference paper or candidate own content/tools.