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Course10210633953 lectures

Computational Genomics

Prof. Vineet Kumar Sharma · IISER Bhopal

Start with lecture 1 At NPTEL

Lectures

week-01

  1. Introduction to Different OMICS Approaches and their Applications Video
  2. Genetic Information in Prokaryotic Video
  3. Databases and Web Resources to Store and Access the Biological Data Video

week-02

  1. First and Second Generation Sequencing Technologies Video
  2. Long Read Sequencing and Linked Read Sequencing - Part 01 Video
  3. Long Read Sequencing and Linked Read Sequencing - Part 02 Video
  4. Sequence Formats and Databases for Genomic Analysis Video

week-03

  1. Introduction to Linux Video
  2. File Handling and Remote Connectivity in Linux Video
  3. Running Linux Commands and Installation of Genomic Packages Video
  4. Introduction to R and Applications in Genomic Analysis Video

week-04

  1. Publicly Available Tools and Need for Workstations for Genomic Analysis Video
  2. Overview of Genomic and Transcriptomic Analysis Video
  3. Genomic and Transcriptomic Analysis of an Organism with Case Studies Video
  4. How to Collect & Confirm Sample of the Species to be Sequenced & Transcriptome Sequencing Approaches Video

week-05

  1. Estimating the Amount of Sequencing Coverage for a Genome and Hybrid Sequencing Approaches Video
  2. Types of Reads, Quality Filtering, Estimating the Genome Complexity and Heterozygosity Video
  3. Genome Assembly and its Completion Status, Assembly Algorithms Video

week-06

  1. Commonly Used Assembly Tools Video
  2. Linked-Read Sequencing and Processing Video
  3. Long Reads Analysis and Assembly Workflow Video

week-07

  1. De novo Assembly Using Genomic and Transcriptomic Reads Video
  2. Merging Assemblies to Create Hybrid Assembly and Determining the Quality of Assembly Video
  3. Chromosomal Level Assembly and Case Studies Video

week-08

  1. Identification and Annotation of Repeats in Genomes Video
  2. De novo Transcriptome Assembly and Making the Coding Gene Set Video
  3. Prediction of tRNA, rRNA and miRNA in a Genome Video
  4. Functional Annotation and Identification of Metabolic Pathways in a Genome Video

week-09

  1. Comprehensive Functional Annotation of Predicted Genes in a Genome Video
  2. Functional Annotation of Predicted Genes by Alternate Methods Video
  3. Methods and Steps to Perform the Evolutionary Analysis of a Genome Video
  4. Methods for Taxonomic Classification and Phylogeny Econstruction and Analysis Video

week-10

  1. Epigenetics, ChIp-seq, Transcriptome and Microarrays for Regulation of Expression Video
  2. Single Cell Genomics, 10X Chromium Linked-reads and Illumina Sequencing, Single Cell Gene Expression Video
  3. Application of Multiomics Approaches in Human Health and Diseases Such as Cancer, Diabetes, etc. Video

week-11

  1. Prokaryotic Genome Sequencing and Assembly Approaches Video
  2. Gene Prediction Approaches and Common Methods for Bacterial Gene Prediction Video
  3. Common Methods for Annotation of a Bacterial Genome, t-RNA, rRNA, Operon Prediction and Annotation Video
  4. Phylogenetic Analysis of Bacterial Genomes Video
  5. Metabolic and Comparative Analysis Video

week-12

  1. Microbiome and Metagenome, Human, Organismal and Environmental Microbiomes Video
  2. Sequencing and Assembly of Metagenomes, Gene Prediction, Annotation, MAGs (Part 1) Video
  3. Sequencing and Assembly of Metagenomes, Gene Prediction, Annotation, MAGs (Part 2) Video
  4. Taxonomic Analysis Using Amplicon Sequence Variants, Statistical Analysis Video

Live Session

  1. Live Session 10-02-2024 Video
  2. Live Session 17-02-2024 Video
  3. Live Session 24-02-2024 Video
  4. Live Session 02-03-2024 Video
  5. Live Session 09-03-2024 Video
  6. Live Session 16-03-2024 Video
  7. Live Session 30-03-2024 Video
  8. Live Session 06-04-2024 Video
  9. Live Session 13-04-2024 Video

Syllabus and materials

At NPTEL, as the course publishes them.

Credits and licence

Institution
IISER Bhopal
Department
Biotechnology
Teacher
Prof. Vineet Kumar Sharma
Level
Undergraduate
Language
English
Subjects
Biology
Source
NPTEL
Licence
CC BY-NC-SA, as NPTEL states it. Non-commercial use only. NPTEL's terms
Attribution
NPTEL states: "Distributed under Creative Commons Attribution-ShareAlike / CC BY - NC - SA", beside a BY-NC-SA badge. Coordinated by IIT Madras.
Who can watch
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