Course details : The course will provide an overview of different techniques related to Next Generation Sequencing. A part of the class will cover and introduction to NGS and explanation of various protocols in common usage.
Why take this workshop?
At present there are no courses that students can use to learn tools and techniques in Next Generation Sequencing. Although the actual sequence generation can be outsourced, students will still have to learn the bioinformatics pipelines to do meaningful analyses. This course, aims to familiarize students with different NGS pipelines in hope that they will be able to conduct advanced, independent research in diverse fields.
A majority of the course will include hands-on practical/lab components that require a computer. A personal laptop is necessary for this workshop.
Module 1: Understanding NGS, platforms and study design:
An introduction to Next Generation Sequencing techniques. Review of different approaches, sequencing platforms, benefits and shortcomings of these platforms.
How to design a genomics study, tradeoffs between number of samples, type & length of read, coverage, depth,Phred score, reference sequence alignment (contigs, scaffolds, N50, L50).
Module 2: Library preparation and Illumina run
Demonstration and sample run of a Illumina MiSeq or similar. May include library preparation steps and an actual run.
Module 3: Diversity of library preparation & protocols
Lab protocols overview (does not involve actual lab work): Protocols to be reviewed - RAD, ddRAD, ezRAD, 2bRAD, UCE, HYRAD, MAB-seq, Exoncap-GBS, SNP-chips and probe designing, whole genome sequencing, enrichment techniques (?)
Module 4: Bioinformatics Pipelines
From STACKS, VCFtools, SAMtools, Plink, bwa, bowtie,GATK, trinity or velvet, (assembly), iPyRAD, PHYLUCE (?), PMDTools (ancient DNA), SNP phasing, SNAPP, SOAP (and variants), Burrows-Wheeler Aligner BWA.
Basics of Python, Bash scripting to enable finding your way around data
Module 5: Phylogenomics: introduction, methods and softwares, RAxML, Phylogenetic Networks, coalescent theory, partitioning, molecular clocks and fossil calibration, bayesian trees MCMC, G-PhoCS.
Module 6: Population genomics:
This module will include introduction to the following analytical tools, some which will be demonstrated through a hands-on workshop with real data : Fast STRUCTURE, ADMIXTURE, NETVIEW, PSMC, ABBA-BABA statistics, ANGSD, Bayescan, MEMGENE, GenAlEx, Coancestry, Geneclass2, NeEstimator, DIYABC.