Next Generation Sequencing (NGS)/Genotyping by sequencing

Genotyping By Sequencing (GBS) is a method of cataloguing genetic variation between individuals on a common reference genome by using Next Generation Sequencing. __TOC__ Overview Genetic variation between individuals is a key component of explaining phenotype, traits or characteristics. For this reason, cataloguing variations between individuals is an important step towards understanding, predicting, and ultimately engineering biology. There are many methods of cataloguing variation between individuals. Genotyping By Sequencing (GBS) being a common method. GBS relies on generating sequencing data for an individual which is aligned to the reference genome. Variations are then called on the reference using a variety of methods. Useful background There are two key 'biological' concepts related to GBS, sequencing, alignment and genotyping. From an informatics perspective, imputation. Objective For a given individual, GBS produces a catalogue of variation for that individual. It is a relatively cheap and 'un-biased' method of discovering variations, not being limited to variations within genes, or transcripts, and without any prior expectation of polymorphic sites. Biological questions Variation from GBS can be used to explain quantitative differences between individuals, better understand genetic relationships between groups of individuals, allow high density genetic maps to be constructed. GWAS. Inputs and outputs Inputs A reference genome Whole Genome Sequencing over one or more individuals. Outputs For each individual, a list of variant loci. Variations may include SNPs, InDels, or Structural Variations, depending on the sequencing technology used. Experimental design There are two broad approaches to GBS, 1) relatively high depth of coverage over N individuals, or 2) relatively low level coverage of N groups of individuals (with relativly high coverage per group). If only short read sequencing technology is used, then only SNPs and small InDels will be discovered. If longer reads and paired-end sequencing technology is used, larger InDels and structural variation may be discovered. Typical steps in the method A bioinformatics workflow for Genotyping by Sequencing (GBS) Sample collection Summary Brief bit of information. Sequencing Summary Brief bit of information. QC and filtering Summary Brief bit of information. Alignment Summary Brief bit of information. Genotype calling Summary Brief bit of information. Data submission Summary Brief bit of information. Next steps Depending on the type of experiment, GWAS, GSEA, Genetic Mapping. Workflows Example galaxy workflow Link to an example galaxy workflow for for the method (including example datasets) on a given galaxy instance or to the XML document describing the workflow. Example command line workflow Discussion POV discussion about the method. Links to related discussion on BioStar: Genotyping By Sequencing