Genotyping by Sequencing (GBS)

GBS is a method for high throughput SNP discovery and also genotyping in large volume of DNA samples. This method is basically a restriction enzyme-mediated complexity reduction followed by sequencing using Illumina platforms to discover random markers across an entire genome.

Eurofins Genomics offers comprehensive sequencing on Illumina platform. We offer customized experimental design of GBS for association and genotyping studies etc. We have developed standard pipeline for advanced bioinformatics analysis of sequencing data and we provide support of experienced scientist for end to end analysis.

Workflow and deliverables

a. Quality check of raw reads:

The raw reads will be subjected to quality filtration and adapter trimming. The primer sequences, poly(A) tails and reads produced from ribosomal DNA templates will be removed. The high quality data will be used for downstream analysis.

b. Mapping Reference Genome.

The high quality reads are mapped to reference genome sequence using bwa. The BAM files further processed using SAMTOOLS. The tag-related statistics are also calculated for GBS data.

c. SNP detection and annotation

The Variant calling is performed using SAMTOOLS variant pipeline, across samples.

Deliverables:

• Quality filtration of reads
• Mapping on the reference genome
• SNP Discovery and annotation
• Compile Report