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Where to outsource next-generation sequencing runs for de novo SNP discovery for phylogenetics and phylogeography

Intro

Given their high density throughout the genome, single nucleotide polymorphisms (SNPs) have become a popular marker for population genetics and phylogenetics analyses in evolutionary biology (in addition to applications in QTL mapping, association studies etc.).  The rapid advance of next-generation sequencing (NGS) has created several new ways of generating 100s to hundreds of thousands of variable SNPs quickly and cost-effectively. 

In this post, I am compiling a list of North American facilities with capabilities for de novo genome-scale data generation and marker (i.e. SNP) discovery.  Virtually all of the services below also provide current-generation Sanger sequencing.  Expect this list to continue to grow as I find more labs and companies that provide services on the NGS market.  I also plan on summarizing cost estimates per sample and lane for freshwater fish samples. Moreover, I intend to maintain this list to keep it continuously updated. 

List of NGS Services for SNP discovery:

ABRF Core Marketplace - AllSeq -Allseq has created a “Sequencing Marketplace” that matches researchers with the appropriate sequencing technology and service providers to meet their needs.  This seems very useful for getting competitive estimates for your NGS platform outsourced work. Click the link above, register and log in to start.  Here is a nice interview article on the Allseq marketplace.

Beckman Coulter Genomics - De novo genome sequencing and transcriptome sequencing, with next-generation sequencing services based on the Roche 454 and Illumina HiSeq platform runs.

Brigham Young University DNA Sequencing Center (DNASC) - Services in next-generation sequencing and genomics based on Roche 454 and Illumina MiSeq platforms.

Eurofins MWG Operon - Services in next-generation sequencing, transcriptome sequencing, bioinformatics and special sequencing-related services.

Floragenex - The self-proclaimed worldwide leaders in RAD sequencing, Floragenex specializes in providing services in restriction site-associated sequencing (RAD-seq) combining digest + massively parallel sequencing with the Illumina platform. (January 2015:) Current pricing is $79/sample for library prep and sequencing under their “Value” service, and $199/sample under their Premium service including sophisticated bioinformatics work up after runs. (April 2016:) Currently, Floragenex has switched to only doing ddRad-seq.

Genewiz - Perhaps the widest range of NGS platforms usually available, including options for de novo sequencing and assembly based on Illumina HiSeq, Illumina MiSeq, Ion Proton™, and Ion PGM™ platforms.

Genohub - Georgia Genomics Facility (GGF) - In addition to genotyping services (e.g. microsatellite DNA marker development and scoring), this core facility provides next-generation sequencing services on Roche 454, Illumina HiSeq, Illumina MiSeq, and Ion Torrent™ platforms, as well as bioinformatics services.

Oregon State University Center for Genome Research & Biocomputing (CGRB) - Services in genomics, biocomputing and bioinformatics, imaging and image analysis.  Roche 454 and Illumina HiSeq and MiSeq platforms.

Science Exchange - [More coming soon.]

SNPsaurus - Provides services for genotyping-by-sequencing using the “nextRAD” method, which differs from other GBS methods in  selectively amplifying fragments across the genome with a select sequence, allowing sequences to stack up only at those regions, which are scattered throughout the genome. This group apparently provides an academic discount for samples with genomes under 1 gigabase in size. I think that based on the name of the method, nextRad refers to Nextera library prep for Illumina platform sequencing. (April 2016:) For 95-sample projects, pricing is $69-99/sample for 15,000-50,000 nextRad loci. For 190-sample projects, pricing is $59-74/sample for the same range of loci.

Look for more updates to this page in the near future!

~J