Genotyping

Genotype your samples with next generation DNA sequencing

Floragenex specializes in the use of next generation DNA sequencing (NGS) methods for genotyping. We offer a host of unique services and technologies that meet wide marker and sample requirements for our clients. 

Why use NGS for genotyping?

Historical marker development projects rely upon an initial discovery effort followed by a genotyping phase to fully genotype samples of interest. While effective, this strategy is slow and subject to ascertainment bias in genetic marker discovery.

Floragenex genotyping services provide an efficient solution for clients seeking to rapidly identify and genotype large amounts of genetic variation in a single, integrated project. Using the power and flexibility of next gen sequencing, a variety of genotyping options are available to the client, depending on their marker requirements and level of support needed


NGS Genotyping Technolgies

RAD Sequencing (RAD-Seq) and SBG / dd-RAD Sequencing (dd-RAD)

  • Genotype as few as 95 to 1000+ samples (in increments of 95)
  • Discover and genotype from 500 to 100,000 single nucleotide variants in a single project
  • Sequenced on the Illumina HiSeq™ family of NGS platforms
  • Can be applied in species with or without genomic resources and reference genome
  • Effective in complex genomes with repetitive structure
  • Minimal ascertainment bias
  • Cost effective with no up front oligonucelotide or array set-up costs

 

AMPLISEQ TARGETED SEQUENCING AND GENOTYPING

  • Target specific variants for genotyping
  • DNA to genotypes in two to three weeks
  • Survey from 96 to 384 SNP variants
  • Flexible project architectures: sequence from 192 to 768 samples
  • Fully automated bioinformatics and analysis
  • Economical pricing competitive with leading genotyping systems

RAD-Seq Genotyping Options

Library Preparation

Preparation packages are for clients that want to take advantage of Floragenex expertise in library preparation.

Preparation projects are the most cost efficient strategy for scientists who know the sequencing they need, want to work with third party sequencing facilities and do not require project planning or bioinformatics support.              

Preparation PACKAGES INCLUDE:

  • Batch processing of 95 samples
  • Choice of library preparation with SbfI or PstI
  • Libraries shipped via courier to your laboratory

Prep and Sequencing 

Prep and sequencing packages are an ideal way for scientists to obtain RAD sequence data at an economical price.

These projects are specifically designed for scientists who are knowledgeable in next generation DNA sequence analysis and do not require extensive project planning or bioinformatics support.                                                                                                                 

Prep and Seq packages include:

  • Batch processing of 95 samples
  • Choice of library preparation with SbfI or PstI
  • Includes library sequencing on single Illumina HiSeq 2000 lane (1x100 bp with ~125 Million reads passing filters)
  • Rapid 12-14 week turn around time

Prep, Sequencing and Analysis

Prep, sequencing and analysis packages are a turnkey solution for scientists that simply want results. 

With these projects, our genomics team provides end to end, comprehensive support for your RAD project, with laboratory processing, assistance in project design and leading bioinformatics support, with data and graphics-rich analytics reporting.

Prep, Seq and Analysis packages include:

  • Batch processing of 95 samples
  • Choice of library preparation with SbfI or PstI
  • Includes library sequencing on single Illumina HiSeq 2000 lane (1x100 bp with ~125 Million reads passing filters)
  • Full bioinformatics support:
    • Next-gen sequencing QA/QC
    • Index / barcode demultiplexing
    • De novo assembly (if required)
    • Alignment
    • Variant calling (SNP)
    • Comprehensive reporting
  • Sequence data can be converted into VCF, JoinMap™, IUPAC, STRUCTURE and other genotyping formats.
  • Up to 12 months of data access
  • 16-24 week turn around time