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Quick Facts

Medium Of Instructions	Mode Of Learning	Mode Of Delivery
English	Self Study	Video and Text Based

Important dates

Start Date : 20 Jan, 2025

End Date : 11 Apr, 2025

End Date : 27 Jan, 2025

Start Date : 27 Apr, 2025

End Date : 14 Feb, 2025

Fees Informations	Certificate Availability	Certificate Providing Authority
INR 1000	yes	IISER Bhopal

Introduction to Computational genomics, Transcriptomics, Proteomics, Epigenomics, Metagenomics and their applications, The BIG data of biological sciences
Organization of genetic information in prokaryotic and eukaryotic cell, genome maps, Eukaryotic genome structure, High-throughput technologies to translate this information into genomic data
How genomic data is organized in public databases, Genomics web resources, Nucleic acid and protein sequence databases, gene expression databases, Metabolic and metabolomic databases. Examples: NCBI GenBank and Expasy, EBI, Ensembl, UCSC, KEGG

First, second generation sequencing technologies including Sanger and Illumina and their data output
Long read sequencing and linked read sequencing (Nanopore, PacBio, TELL-Seq)
Sequence formats: FASTA, GenBank, EMBL, XML, Fastq, fast5, etc., genomic database versions and archives, NCBI SRA, bio-project, accessions, data retrieval using wget, FTP, FileZilla, and scripts provided by the database team for genomic analysis

Introduction to genomes and packages for genomic analysis such as EMBOSS; Specifications of workstations needed for genomic analysis, Introduction to High Performance Computing and servers, and their need in genomic analysis
Overview and concepts in genomic and transcriptomic analysis of an organism with examples and case studies
Sample collection, DNA extraction and quantification, and species identification of the species to be sequenced. RNA extraction and transcriptome sequencing approaches

Methods to estimate the amount of sequencing coverage needed for genomic assembly, use of hybrid sequencing approaches for appropriate coverage and assembly
Short and long reads, paired-end reads, quality filtering of sequence data, Genome complexity assessment, Jellyfish and GenomeScope for generating k-mer count histograms and calculating genomic heterozygosity
Concept of genome assembly, contigs, scaffolds, complete genome, draft genome, chromosomal level assembly, Genome assembly algorithms such as De-Bruijn graph, Overlap layout consensus (OLC), Hybrid assembly

Introduction to common assembly tools ABySS, SOAPdeneno, Flye, Supernova
10X genomic linked-read sequencing, use of proc10xG set of python scripts to pre-process the 10x Genomics raw reads, removal of barcode sequences
Nanopore long reads analysis: Guppy for base calling of raw reads, adaptor removal using Porechop, Genome assembly workflow using three different assemblers: wtdbg, SMARTdenovo, and Flye, parameters for assembly

de novo assembly using Supernova, parameters, usage of genomic and transcriptomic reads to increase assembly contiguity
Merging assemblies to create hybrid assembly, gap closing of assembly and polishing, fixation of small indels, base errors, and local misassemblies, determining the quality of assembly using N50, BUSCO scores, coverage etc.,
Chromosomal level assembly using Hi-C, concept of reference genome, finished genome, draft genome, case studies

Annotation of repeats in final genome assembly using RepeatMasker, Determining the simple and complex repeat content of a genome
de novo transcriptome assembly, Determining the coding gene set using MAKER pipeline
Prediction of tRNA, rRNA and miRNA in a genome, Identification of metabolic pathways by KEGG

Comprehensive functional annotation of predicted genes or protein sequences by homology-based alignment using Blast or Blat, COGs, Gene ontology based annotation, Interproscan, PROSITE, Pfam, prints, patterns, motifs and fingerprints
Evolutionary analysis using homologs, paralogs and orthologs, Multiple signs of adaptation, gene family expansion and contraction
Taxonomic classification, marker sequences such as 16S rDNA and ITS, taxonomic hierarchy, Phylogeny reconstruction using multiple sequence alignment, Distance based approaches such as Neighbour joining, Character based approaches such as Maximum parsimony, Maximum likelihood, RAxML

Epigenetics, ChIp-seq, transcriptome and microarrays for regulation of expression
Single cell genomics, 10X Chromium linked-reads and Illumina sequencing, single cell gene expression
Application of multiomics approaches in human health and diseases such as cancer, diabetes, etc.

Prokaryotic genome sequencing and assembly approaches, draft and complete genomes, taxonomic identification
Gene prediction approaches and common methods, annotation of a bacterial genome, t-RNA, rRNA, operon prediction
Phylogenetic, metabolic and comparative analysis