ddRAD genotyping

A quick and reliable method chosen by IGATech for genotyping-by-sequencing. ddRAD (double digest Restriction Associated DNA) provides complexity reduction by selecting genomic DNA fragments generated by cleavage of both restriction enzymes followed by accurate size-selection. We developed a highly reliable pipeline of simultations and protocol optimization. With any genome size it is possible to maintain control on final per-locus coverage and ensure recall.

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Technologies
NovaSeq6000
Nucleic acids extraction
Reduced-Representation libraries

Features and benefits

  1. Ascertain bias-free experiment
  2. Discover and genotype diversity in one experiments
  3. Customized and reproducible selection of genomic loci
  4. Scalability of markers yield from thousands to hundreds of thousands
  5. High recall rate

Services

  1. DNA extraction service
  2. DNA normalization
  3. Library preparation and QCs
  4. 150bp paired-end sequencing
  5. Data analysis to genotype tables
  6. Complementary analyses:
    • linkage - QTL mapping
    • association studies (GWAS)
    • molecular barcoding / varietal identification
    • diversity and population structure​

Pricing guidelines

Sample number Standard complexity (ca. 30k loci) High complexity (ca. 100k loci)

Standard bioinformatics

(with reference genome)

96 60 euro/sample 85 euro/sample 8 euro/sample
192 55 euro/sample 75 euro/sample 7 euro/sample
288-384 45 euro/sample 65 euro/sample euro/sample
480-864 39 euro/sample 57 euro/sample euro/sample
960+ 35 euro/sample 54 euro/sample euro/sample

 

Less is more

We were able to make an excellent map to anchor our genome assembly. IGATech support was very helpful.

Mark Aarts
Associate Professor in Plant Genetics 
Wageningen University (Netherlands)
 

One of the major benefits of low error rate provided by Illumina platform is their utilization for accurate SNP calling. However, for large scale experiments where cost-effectiveness has to cope with massive panel of samples (breeding, ecology, association-studies, etc.), whole genome sequencing remains an unaffordable option. One of the most effective techniques in the cutting down of such cost is to reduce the genome to a fraction of its size before sequencing

The method of choice adopted by IGATech for genotyping-by-sequencing is the so-called ddRAD (double digest Restriction Associated DNA). The system provides complexity reduction by selecting genomic DNA fragments generated by cleavage by both restriction enzymes, one per side. This has the advantage of having each genomic locus characterized by a specific size in the library of fragments. Adopting in silico simulation it is possible to fine-tune the amount of genomic loci to be selected. 

AN "OPEN SYSTEM"

Genetic variability is sampled unbiasedly

This capability allows to accommodate the adequate sequencing yield to obtain effective coverage to most of loci and thus providing high and reproducible genotyping ratio across individuals also in large cohorts. Moreover, compared to array-based solutions, sequencing is an “open system”, meaning that genetic variability is sampled unbiasedly: this has a critical impact on experiments involving genetic backgrounds and haplotypes not exhaustively represented by the panel of markers used in an array or any previous experiment.

 

Over the past years we came to heavily rely on the excellent services provided by IGATech, whose expertise, efficiency, helpful and custom-oriented attitude accompanied us in our scientific growth in the field of genomics. A recent service extension is their double enzyme ddRAD Seq approach we are currently using with great success in several crop species.

Prof. Mario Enrico Pè 
Director of the Institute of Life Science,
Scuola Superiore Sant'Anna, Pisa (Italy)

Expertise

IGATech has successfully conducted many genotyping-by-sequencing experiments on both plants and animals, with genome size ranging from hundreds of megabases to tens of gigabases. Despite such very big differences in genome size and complexity we managed to obtain effective complexity reduction and to have more than 95% of sequencing data in loci with adequate coverage overall. This why our internally developed protocol is also suitable for the finding of discriminatory marker for varietal identification and contamination levels estimation also in food substrates. Our lab practices are devoted to obtain reproducible experiments and our bioinformatics analyses to obtain high quality data points. Our internal barcoding system allows reaching a virtually unlimited multiplexing. We provide tailored consultancy for every project to make sure the outcome will meet our customer expectations. Every genome and experimental design have its challenges.

 

 

 

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Documents & Reports

Human samples clearance

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Terms and Conditions v04.pdf

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Privacy Information

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Samples Spreadsheet v7.xlsx

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ddRAD Data delivery specifications.pdf

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ddRAD-target flyer.pdf

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Genotyping Sample requirements guidelines v01.pdf

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