Genotyping By Sequencing/ddRAD sequencing
NGB diagnostics offers multiple restriction enzyme based genome reduced representation sequencing called Genotyping by sequencing or Restriction associated digestion & Sequencing (RAD sequencing).
Genotyping by Sequencing (GBS) is the cost effective method of choice for genome wide SNP discovery/genotyping with or without prior knowledge of the genome sequence
Applications of GBS/ddRAD:
- Co-dominant SNP Genotyping
- Genetic Diversity Analysis
- Genetic Mapping
- QTL Mapping
- Bulk Segregant Analysis
- Mapping to Whole Genome Sequence
- Discovery of (rare) SNP variants
- Genome Wide Association Mapping
- Genomic Selection/Prediction
We currently offer:
- Single or double digest Libraries.
- The library multiplexing of samples ranges from: 24 Plex, 48 plex, 96 plex, 192 Plex and upto 384 Plex.
- Sequencing on Illumina HiSEQ 4000/ NextSEQ 500 with read length 150x2 paired end reads.
- Standard bioinformatics Included.
Standard GBS/ddRAD Bioinformatics:
Quality Control
- Raw data QC.
- Removal of low quality reads and trimming of Low quality bases.
- Adaptor trimming.
WGBS/ddRAD Analysis:
- For Non-Reference based: Creation of non redundant Unique TAG Reference & Then map raw reads of each sample followed by SNP calling.
- For Reference based: Mapping of Filtered data to reference followed by SNP and In-del calling.
- SNP calling available using: GATK toolkit or Freebayes algorithm.
- SNP filtering using TASSEL v5 for minor allele frequency and Missing data.
- For biparental populaitons: Linkage Mapping using Joinmap and QTL analysis using windows QTL cartographer.
For Association Analysis:
- LD analysis, QTL analysis using GLM, MLM method, Manhattan plots, QQ plots, using TASSEL.
- Population structure using Structure software.
- GAPIT for pedigree analysis.
- IBD, IBH analysis using Beagle.
