University of Illinois
High-Performance Biological Computing

Services and FEES

HPCBio will produce a quote for each project that it is asked to undertake. This quote is specific to the project, and based on the size of the dataset to be analyzed, the amount of staff time required to process and analyze it, and the computer resources that will be needed to perform the work. Our prices are strictly based on a cost recovery model; the fees you pay will not subsidize our other activities.

Here are some examples of genome/transcriptome sequencing analysis services that are offered through HPCBio and typical associated costs. Please note that these prices are purely indicative, individual quotes will be provided for specific projects.

• Genome sequence assembly
  De novo assemblies using next generation sequencing data from Illumina and Roche 454 (typically 50x coverage). $250 for a bacterial genome (<10 MB), $600 for an insect genome (100-500 MB), $2000 for a vertebrate genome (1-5 GB).
   
• Transcriptome sequence assembly
  De novo assemblies using next generation sequencing data from Illumina and Roche 454. From $500 to $5000 depending on the number of genes, the sequencing technology used (Illumina HiSeq or MiSeq, Roche 454), and the total number of available reads.
   
• Annotation of genomes or transcriptomes
  Includes ab initio gene prediction on the assembled contigs followed by annotation based on sequence similarity to existing database sequences. We use the MAKER environment to customize annotations. $200 for a bacterial genome, $500-1000 for an insect genome, $1000-2000 for a vertebrate genome, $200-1000 for transcriptomes. The cost varies based on the number of annotation criteria used (e.g. InterProScan, multiple BLAST databases, multiple ab initio predictors, availability and quality of reference genome and transcriptome data, available ESTs, etc.)
   
• RNA-seq analysis
  Differential gene/transcript expression analysis based on gene counts or RPKM values. Generation of the gene counts: $150/sample, based on 20-30M reads/sample. Statistical analysis: $200 setup + $40/sample.
   
• Molecular marker discovery
  Includes single nucleotide polymorphism, indels, simple sequence repeats discovery, extract molecular marker flanking sequences for designing genotype assays, and annotation of the markers. Since the complexity of individual projects can vary greatly, it is impossible to provide a typical cost.
   
• ChIP-Seq analysis
  Identification of putative transcription factor binding regions, retrieve neighboring gene context, and annotation of binding regions. $150/sample for mapping reads to the genome and peak calling; additional analyses charged on an hourly basis.
   
• Metagenomic analysis
  Alignment of 16S rDNA sequences to reference database (RDP), assignment of OTUs, $5/sample; additional statistical analyses on a case by case basis.
  De novo assemblies of metagenome data, annotation of the assemblies, and MEGAN phylogenetic analysis, priced on a case by case basis.
   
• Microarray analysis
  Includes data preprocessing, statistical tests, database, annotation and data mining on different platforms (cDNA, Oligo, and Affymetrix) using statistical program R (Bioconductor). $200 setup fee, then $40/sample.

Please contact HPCBio for specifics on procedures and deliverables. These are being constantly revised and improved to keep pace with advances in bioinformatics, software, and computer infrastructure. We are open to customizing protocol and deliverables to your project. 

***This is an abridged list of our service prices and subject to change at any time; please contact Dr. C. Victor Jongeneel, Director of HPCBio, at (217) 244-1795 or vjongene@illinois.edu for information on prices and other issues related to your project.***

Fees for facility users from universities other than the University of Illinois or other State of Illinois Universities are 25.4% above on-campus rates., For projects from off-campus users exceeding $5,000 a contract must be negotiated through the Grants & Contracts Office of the University of Illinois. Contact Dr. Mark A. Mikel (217.244.0144, mmikel@illinois.edu), Associate Director of the Roy J. Carver Biotechnology Center, to for further information.

*All services are provided on a best effort basis and must be paid regardless of failure or success unless stated otherwise*

All work performed by HPCBio should be acknowledged in scholarly publications, posters, and presentations. Proper recognition allows us to measure the impact of our work and supports our initiatives in obtaining sponsored funding. In addition, any personnel who make a substantial intellectual or experimental contribution are deserving of further recognition as co-author.