Ngs Summer Training

NTHRYS provides Ngs Summer Training for interested candidates at its Hyderabad facility, Telangana. Please refer below for more details including Fee strctures, Eligibility, Protocols and Modules etc.,. Please do call / message / whatsapp for more details on 9014935156 [India - +91]

Eligibility: BSc / BTech / MSc / MTech / MPhil / PhD in any Life Sciences studying or completed students

Protocols / Techniques Covered

Topic	Description	Tools
Introduction	Data Types, data formats -(Fastq, Qseq etc. most of the types including color space) Understanding raw read data from the NGS sequencers
Understanding NCBI, PUBMED,MESH and CDD	NCBI, PUBMED,MESH and CDD
Sequence alignment and its application	Introduction Algorithms Multiple sequence alignment	BLAST FASTA Needleman wunch Smith waterman Clustal omega t-coffee
Genomics	Introduction with gene databases-GENE, SNP Genome Annotation and Visualization Gene finding and function prediction General introduction to Gene expression in prokaryotes and eukaryotes, transcription factors Binding sites ( SNP, EST, STS)	GENSCAN
ORF finder and its application	Online tools with ORF	ORF finder
Gene Prediction AND Expression	Introduction to gene and gene prediction Determine Beginning and end positions of gene in genome and gene structure Codons; Discovery of split genes; Exons and Introns; Splicing;	Human Splicing finder GenMark and GenScan
Phylogenetic tree-detail	Definitions of homologues, orthologues, paralogues Methods of phylogenetic analysis: UPGMA, WPGMA,  neighbour joining method, Maximum likelihood	PHYLIP MEGA Tree finder
Next Generation Sequencing Technology	What is NGS? And Basic concepts Sequencing Methods Platform overview and Biological applications Recent scientific breakthroughs using NGS technology Applications	Illumina hi seq mi seq phylogenetic analysis MUMmer 3.12
Introduction to Sequencing	Traditional Methods Sanger sequencing Drawbacks of Sanger’s sequencing
NGS Data Generation	Generation of large scale molecular biology data
Next Generation Sequencing Methods	Concept of sequence quality scores (Overview of  Phred, Illumina, SoliD sequencing) Issues and Filtering Next-Gen data (coverage, depth, short-reads, Chimeras) Emulsion based PCR and polonies SAM tools and SAM alignment format Single molecules sequencing methods. Applications of High throughput sequencing methods.
NGS Data Analysis	Alignment and mapping highlighting differences with conventional alignment, tools used and brief parameters (BWA, Bowtie, MAQ, etc) Brief Concepts of ChiP-seq, DNase-seq, MNase-seq, RNA-seq. Transcript Assembly and gene expression (RNA-Seq) with tools like Tophat/Cufflinks Variation detection (DNA-Seq and Exome sequencing) Protein Binding Site detection (Chip-Seq) with tools like MACS CpG Islands and Methylaion Patterns (Bisu lphite-Seq) with tools like bismark
Genome Databases and File Formats	Databases File formats	GENEBANK GENE SNP fast q gbk
Galaxy	How to upload data Explore published histories Generate new history Changing dataset formats and editing attributes	SRA data FTP download SAM tools
Data processing	Analysis workflow Sequence quality evaluation Alignment theories Data formats and Data visualization to explore various NGS nodes	FastQC BLAST All Stand alone Blast SAM tools Bed Format
DNA-Seq	Genetic variation Variant Calling using various methods Variant Annotations	GATK Snver VarScan Picard SAMtool
RNA-Seq	Biological theories on RNA-Seq experiments Alignment Gene expression analysis Alternative splicing Transcript variation Allele-specific expression	BlAST All Standalone blast
ChIP-seq	Biological theories on ChIP-seq analysis DNA fragment evaluation Peak identification	Trimmomatic FAST QC
NGS Data Visualization with Exploration with IGV	View, Navigate and Browse large dataset Visualize specific region on Genome and View Alignment	BLAST



Topics Covered for various durations:

5 Days - Topics 1, 9, 11, 15 and 16 + (Optional Minor Project)

10 Days - Topics 1, 4, 8, 9, 10, 11, 12, 14 and 16 + (Optional Minor Project)

20 Days - Topics 1, 4, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17 and 18 + (Optional Minor Project)

30 Days to 45 Days - All Topics Mentioned above + (Optional Minor Project)

3 Months - All Topics mentioned above + Minor Project (On Live Secondary Research Data), Fee Rs 25000/- additional to 45 Days Module

6 Months - All Topics mentioned above + Publication Project (On Live Secondary Research Data - This project will be guided by respective research guides to get published in respective Scopus or Science Citation Indexed Journals. Research Design for the Publication Project will be provided by NTHRYS Research Panel), Fee Rs 65000/- additional to 45 Days Moduel

Fee Structures for Ngs Summer Training