Next Generation Sequencing (NGS)

Introductory course on Next Generation Sequencing (NGS) technologies and the analysis tools and workflows required for analyzing short read data Introduction: This course teaches biologists how to analyze data from Next Generation Sequencing (NGS) platforms. Topics include the description of sequencing strategies and platforms, experiment types, data formats, and command line tools for various workflows, such as quantification of transcripts, alternative splice forms, copy number variants, single nucleotide polymorphisms, etc. Why learn NGS? The genomics field is exploding with NGS data and there are many discoveries to be made. Researchers need to be able to analyze data themselves and stay up to date with the methods and tools. Logistics: The course is divided into 8 sessions with pre-recorded videos, handouts, reference cards, examples, data, scripts and quizzes. Enrollees can contact the instructor with questions and get help on the projects. The main topics are listed below, but we teach mostly everything there is to know about NGS analysis. Homework assignments will involve running commands learned in the live lectures. The course is divided into 4 sessions. Homework assignments will involve running computationally intensive tools Requirements:Basic molecular biology and biochemistry Price: $2400 for Commercial/Government enrollees and $1200 for Academic researchers and students Instructor: Shailender Nagpal Tools required: SRAtools (Converting SRA data to FASTQ), FASTQC, FastX, CrossBow, SnpEff, Bowtie, Samtools, BWA, MAQ, BEDTools Syllabus: - - Introduction to various NGS technologies/platforms, experiment types and applications - - Working with reads, alignments, quality scores, etc - - Algorithms and tools for NGS read alignment, SNP calling - - Various file formats such as SAM, VCF, BED, WIG, PILEUP - - Four different workflows for mutation discovery (CrossBow, Bowtie, BWA, MAQ) - - Functional consequences of variation (SIFT, POLYPHEN) - - TopHat and Cufflinks for RNA-seq, Finding novel transcripts, Expression of splice variants