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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.  These include sequence data from:

  • Illumina HiSeq and MiSeq (50x coverage or more)
  • 10x Genomics data (using Supernova)
  • Long-read sequencing data from Oxford Nanopore and Pacific Biosciences (using Canu, FALCON, or MaSuRCA)

These are general prices:

  • $500-800 for a bacterial or small fungal genomes (<15 MB)
  • $1500 for an insect genome (100-500 MB)
  • $4000 for a well-behaved (homozygous diploid) vertebrate genome (1-2 GB) 

We highly recommend performing an initial shotgun sequence analysis (20-25x coverage) for organisms where little information is known about ploidy or heterzygosity.  This is used in a k-mer-based analysis to determine how difficult the assembly may be.  We can run a k-mer abundance profile and additional quality metrics to determine how difficult the assembly would be.

For bacterial genome assemblies we are now including Prokka-based annotation for no additional cost.

We can also perform followup quality assessment of assemblies against closely-related reference genomes for additional cost.  Please contact us for more details if you are interested.

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), and the total number of available reads.

Assemblies can be evaluated using RSEM and other tools along with input sample information to assess transcript abundance.  Please let us know if you are interested in this.

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 but can also assist in using alternative annotation pipelines, including Prokka or JGI's IMG pipeline.

  • $500-1000 for a small genomes (bacterial, small yeast)
  • $2000-4000 for an insect genome
  • $4000-5000 for a vertebrate genome
  • $1000-2000 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 normalized values.
  • Generation of the gene counts: $240 setup + $40/sample, based on 20-30M reads/sample.  Per-sample costs decrease over 20 samples.
  • Statistical analysis: $300 setup + $60/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.

  • $300 setup + $50/sample for alignment of ChIP-Seq data followed by PCR duplicate marking and basic quality assessment of aligned input/IP data (reads mapped, multi-mapped reads, # duplicates)
  • $20/sample extra for additional quality assessment of samples (coverage correlation analysis, strand cross-correlation, PCR bottleneck visual inspection)
  • $20/sample extra for peak calling (MACS2, EPIC/SICER, or a similar tool).  Please let us know in advance if you have a preference for a particular tool.
  • $300 setup + $60/sample for differential binding statistical analysis (using csaw or similar R/Bioconductor tool)
  • Additional analyses (TSS, MEME/MAST, etc) charged on an hourly basis.

Amplicon Surveys/Metagenomic Analysis

  • Fluidigm analysis: $250-350 per amplicon region using the IM-TORNADO pipeline
  • Other amplicon analyses: $500-1000 per amplicon region for data processing
  • Additional statistical analyses on a case by case basis.

De novo assemblies of metagenome data, annotation of the assemblies, taxonomic/functional classification of raw read data, and other related analyses are also possible and are priced on a case by case basis.

Microarray Analysis

Includes data preprocessing, statistical tests, and inclusion of easily available annotation information for any array type (cDNA, Oligo, and Affymetrix) using statistical program R (Bioconductor). $300 setup fee, then $60/sample. Additional data mining, including gene clustering, GO and KEGG testing are available on a consultation basis ($59/hr).

Other Analyses

We have experience with additional analyses not listed above, including ATAC-Seq, HIT-CLIP, MeDIP/MDB-Seq, Tn-Seq, shRNA, chromosomal replication, and custom pipeline development and optimization.  We can charge on a per-hour basis ($65/hr).  If you have a more complex project, please contact us to discuss additional options for payment.

Also, let us know if you have specific needs 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 protocols and deliverables to your project. 

 

***This is an abridged list of our service prices and subject to change at any time; please contact our Help Desk (hpcbiohelp@igb.illinois.edu) for information on prices and other issues related to your project.***

Facility users other than State of Illinois institutions are subject to a 28.6% indirect cost rate for federally funded projects . State of Illinois non-Federally funded projects are subject to a 21.9% indirect cost rate.  For off-campus projects exceeding $5,000, a contract must be negotiated through University of Illinois Grants and Contracts.  For further information contact Dr. Mark A. Mikel (217-244-0144; mmikel@illinois.edu ), Associate Director of the Roy J. Carver Biotechnology Center.

*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.