Service Descriptions

General Information

IRCF services are continuously being refined. Prices and descriptions of services may be slightly different than listed below. Additionally, the default service methodologies can be modified to suit a client's analysis needs. Simple modifications to default pipelines usually do not incur an additional fee. Please keep in mind that the IRCF can implement novel analyses not listed below using software of a client's choice. Any additional fees associated with novel analyses, including the cost of commercial software, if necessary, will be passed to the client.

Finally, this is not an exhaustive list of the services we provide. Please contact us if you are interested in a bioinformatics analysis not listed on this page.

Please direct any questions about IRCF services to Scott Givan.

Pricing for University of Missouri Clients

Clients with an affiliation to the University of Missouri pay a slightly lower price. Please contact Scott Givan directly for specific pricing information.


Gene Expression Analysis

Description of Service

The default RNA-Seq analysis service includes a rigorous quality control module followed by the TopHat Suite of software. Other analysis software is available by request; including: HTSeq, DEseq and EdgeR. The default deliverable is a spreadsheet of data that includes various gene expression and statistical measures. Additional analysis and visualizations are available for an additional fee.

Pricing

$295 per sample. Volume discounts are available. Contact Scott Givan.

Gene Expression Analysis Interpretation Package

Description of Service

This service, which is distinct from our Gene Expression Analysis service, provides a more extensive exploration of gene expression data and includes Gene Ontology (GO) enrichment analysis, KEGG pathway analysis and publication quality figures.

Pricing

$885 per 4 sample types


Genome Assembly: Prokaryote

Description of Service

The default genome assembly service includes a rigorous quality control module followed by the application error-correcting software. HTS reads are assembled using several programs; including: MaSuRCA, ALLPATHS-LG, Ray, SPAdes and SOAPdenovo. Subsequently, the quality of the separate genome assemblies is determined via summary statistics; i.e., # of contigs, N50, longest contig, as well as statistical methods such as FRC. The deliverable is a fasta file of contigs from the best assembly.

Pricing

$1,475 per assembly.


Genome Assembly: Eukaryote (nuclear)

Description of Service

The default genome assembly service includes a rigorous quality control module followed by the application error-correcting software. HTS reads are assembled using several programs; including: MaSuRCA, ALLPATHS-LG, Ray, and SOAPdenovo. Subsequently, the quality of the separate genome assemblies is determined via summary statistics; i.e., # of contigs, N50, longest contig, as well as statistical methods such as FRC. The deliverable is a fasta file of contigs from the best assembly.

Pricing

$2,950 per assembly.


Genome Assembly: Plastid, Mitochondrial, Viral

Description of Service

The default genome assembly service includes a rigorous quality control module followed by the application error-correcting software. HTS reads are assembled using several programs; including: MaSuRCA, ALLPATHS-LG, Ray, and SOAPdenovo. Subsequently, the quality of the separate genome assemblies is determined via summary statistics; i.e., # of contigs, N50, longest contig, as well as statistical methods such as FRC. The deliverable is a fasta file of contigs from the best assembly.

Pricing

$442.50 per assembly.

Genome Annotation: Prokaryote

Description of Service

The default genome annotation service includes the application of custom and publicly available software to identify and refine gene structures and assign functional information to each gene. Typical publicly available tools include Glimmer3, tmhmm, ELPH and tRNAscan-SE. Several sequence databases are searched to gather functional data; including UniProtKB/Swiss-Prot, Pfam and COGs. NCBI NR is specifically avoided. There are several deliverables:

  1. Fasta files of the genes and proteins identified in the genome
  2. A password-protected website containing a variety of tools (below), which is hosted by the IRCF
  3. BLAST-able sequence databases
  4. A genome browser minimally containing tracks for genes
  5. A searchable annotation database
  6. A metabolic reconstruction tool based on KEGG pathway maps
  7. A custom analysis of COG content of the annotated genome

Pricing

$1,019.58 per genome + $100 per year for lifetime of website.


Genome Browser Setup & Deploy

Description of Service

Set up and deploy a genome browser for a pre-annotated genome. The genome browser instance will be hosted by the IRCF on a password-protected website that can be made publicly available. Up to 4 tracks of available annotation data are included in the base fee. Additional tracks can be loaded for an additional fee. Additionally, a maintenance fee will be collected annually for the lifetime of the genome browser.

Pricing

$368.75 per instance + $50 per year for the lifetime of the genome browser.


RNA-Seq Visualization

Description of Service

In a pre-existing IRCF genome browser instance, upload up to 4 tracks containing RNA-Seq data. More tracks can be uploaded in sets of 4. Input data consists of BAM or SAM files of aligned RNA-Seq reads to the reference genome. The BAM files will be processed and uploaded to a custom plugin that displays the RNA-Seq data in several different formats within the genome browser.

Pricing

$147.50 per set of 4 genome browser tracks.


Transcriptome Assembly: Prokaryote

Description of Service

This service subjects input RNA-Seq sequences to a rigorous quality control module followed by assembly using the Trinity software. Subsequent to various filtering and exclusion techniques a set of assembled transcripts are passed through an automated annotation pipeline to collect and assign functional information to each transcript. The primary deliverable is a fasta file of annotated transcripts. Other deliverables are available, including spreadsheets of annotation data.

Pricing

$1,180 per transcriptome.


Transcriptome Assembly: Eukaryote

Description of Service

This service subjects input RNA-Seq sequences to a rigorous quality control module followed by assembly using the Trinity software. Subsequent to various filtering and exclusion techniques a set of assembled transcripts are passed through an automated annotation pipeline to collect and assign functional information to each transcript. The primary deliverable is a fasta file of annotated transcripts. Other deliverables are available, including spreadsheets of annotation data.

Pricing

$1,917.50 per transcriptome.


Microbial Community Analysis

Description of Service

The input data is typically a barcoded Illumina MiSeq amplicon sequence data, though HiSeq or 454 reads can be used as well. Input reads will be cleaned, chimera removed, and then clustered into OTU's using usearch7. Within- and between-sample OTU abundances will be estimated and summarized using a standard QIIME methodology. The primary deliverable is a web archive containing tables (including the number of reads per OTU-sample), graphs and figures as generated by Qiime. Other analyses are available upon request for an additional fee.

Pricing

$288.73 per 96 samples (minimum price is $288.73).

Microbial Community Analysis Interpretation Package

Description of Service

This is an extension of the Microbial Community Analysis and provides a more thorough exploration of the composition and potential differences between microbial communities based on metagenomic data. Primary deliverables are publication quality figures and all associated data used to generate the figures. Typical software used to generate the figures include: QIIME, LEfSe, PICRUSt, and HUMAnN. Script customization and ad-hoc analysis are also very common.

Pricing

$1475.00 per experiment


Ad-hoc Services

Description of Service

IRCF staff have wide-ranging experience and expertise. Thus, many ad-hoc services are supported; including (but not necessarily limited to): eukaryotic genome annotation, RAD-Seq analysis, GBS analysis, cryo-EM image analysis, software design & creation in a variety of programming & scripting languages, computational hardware design & implementation and project design and assessment.

Pricing

$73.75 per hour.