Services and Pricing

• Pipeline: raw data quality control and alignment to a reference genome, followed by gene expression quantification, normalization, and correction of batch effects (if necessary)
• Downstream analyses (as applicable): Differential expression analysis (with at least 3 replicated per condition), pathway and gene ontology analysis (for common model species only or gene sets provided by the investigator), weighted gene coexpression network analysis (WGCNA, ≥15 samples)
• Internal rate (for units on MSU campus): $84/hour + data storage fee. Our standard analysis pipeline requires 12 hours ($1,008), or 16 hours with WGCNA ($1,344). Complex experimental designs may require additional time.
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour + data storage fee. Standard analysis pipeline requires 12 hours ($1,320), or 16 hours with WGCNA ($1,760). Complex experimental designs may require additional time.

• We can accommodate data generated by 10x Chromium, Drop-Seq, Smart-Seq, or CEL-Seq among other technologies
• Pipeline: Raw data quality control and alignment, followed by quantification, feature selection, normalization, and correction of both batch and common biological confounding effects (such as cell cycle), cell clustering and visualization, identification of cluster enriched genes.
• Downstream analyses (as applicable): Cell-type annotation, differential expression analysis, GO/pathway enrichment analysis (for well annotated organisms or gene sets provided by the investigator)
• Internal rate (for units on MSU campus): $84/hour + data storage fee
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour + data storage fee

• Data generated by droplet based (10x Chromium) protocols as well as micro-fluidics/-well (Takara, Fluidigm) and combinatorial indexing
• Pipeline: Raw data quality control and alignment, peak calling and quality control, annotation of peaks to genes, feature selection, normalization and dimension reduction, cell clustering and visualization, gene activity interpolation including feature selection, normalization and batch correction as needed.
• Downstream analyses (as applicable): Differential chromatin accessibility per cluster, integration of gene activity data with expression data from scRNA-Seq, enriched motif analysis (for common model species only, unless specific motifs are supplied), GO/pathway enrichment analysis (for well annotated organisms or gene sets provided by the investigator), track visualization with an open-source genome browser.
• Internal rate (for units on MSU campus): $84/hour + data storage fee
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour + data storage fee
   

• Pipeline: Sequence quality control, amplicon sequence variant (ASV) table construction, taxonomy assignment and taxonomic composition analysis
• Downstream analyses (as applicable): Alpha and beta diversity analysis and differential abundance testing
• Internal rate (for units on MSU campus): $84/hour + data storage fee. Our standard analysis pipeline requires 12 hours ($1,008). Complex experimental designs may require additional time.
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour + data storage fee. Standard analysis pipeline requires 12 hours ($1,320). Complex experimental designs may require additional time.

• Read quality control and host decontamination
• Metagenomic assembly
• Gene prediction and functional annotation (ie antibiotic resistance gene detection)
• Genome binning and taxonomic classification
• Diversity and differential abundance analysis (functional and taxonomic)
• Internal rate (for units on MSU campus): $84/hour + data storage fee
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour + data storage fee

• Standard analysis: QC of reads, mapping to reference, identify SNPs (single nucleotide polymorphisms) and indels (short insertion and deletions) using tools like GATK, BCFtools, ANGSD, etc.
• Additional options:
  • Identification of larger structural variants (inversions, duplications, etc.). This type of analysis has specific data requirements so, if possible, talk with a consultant ahead of data collection if this is a research goal.
  • Genotype imputation and haplotype phasing.
  • Genotype recoding for genetic mapping software.
• Downstream analyses: as applicable, such as genotype recoding for genetic mapping software
• Internal rate (for units on MSU campus): $84/hour + data storage fee
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour + data storage fee

• For both PacBio's SMRT and ONT's nanopore sequencing
• Pipeline: basecalling, QC, read error correction, assembly with refinement, alignment, etc.
• Downstream analyses: as applicable, such as detection of transgenes
• Internal rate (for units on MSU campus): $84/hour + data storage fee
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour + data storage fee

• Pipeline: Raw data quality control and alignment to a reference genome, generation of peak calling, annotation of peaks to genes, track visualization with an open-source genome browser.
• Downstream analyses (as applicable): Sample correlation analysis, enriched motif analysis (for common model species only, unless specific motifs are supplied), differential peak calling, pathway and gene ontology analysis (for common model species only, or gene sets provided by the investigator).
• Internal rate (for units on MSU campus): $84/hour + data storage fee.
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour + data storage fee

• Pipeline:
  • Array-based methylation data: background correction and dye bias correction, followed by normalization, batch effect correction, probe-type bias correction, filtering of low-quality data points, and imputation.
  • Bisulfite sequencing data (raw .fastq files): quality control and alignment, followed by methylation calling and filtering CpGs.
• Downstream analyses (as applicable): Differentially methylated regions (DMRs) and/or differentially methylated CpG sites (DMCs) analysis, annotation of DMRs/DMCs with genes or gene sets.
• Internal rate (for units on MSU campus): $84/hour + data storage fee
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour + data storage fee

• Pipeline: Conversion of raw MS data from mzXML to MALDIquant format, followed by peptide/protein identification, protein abundance quantification, filtering, normalization, and missing value imputation.
• Downstream analyses (as applicable): Differential protein expression analysis, protein set enrichment analysis, machine learning-based sample clustering, and protein-protein interaction networks.
• Internal rate (for units on MSU campus): $84/hour + data storage fee
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour + data storage fee

• Examples of analyses that can be performed using population resequencing data follow:
• Estimation of allele frequencies and genetic diversity.
• Inbreeding, relatedness, and genetic load.
• Characterization of population genetic structure.
• Demographic inference. We can help estimate population histories, e.g. population size changes and migration rates through time.
• Genomic selection scans (to identify adaptive loci for example).
• Association trait mapping. We can help identify the genetic architecture and particular loci underlying traits of interest through GWAS (genome-wide association study)-type approaches and divergence scans.
• Phylogenetic and comparative genomics.
• Internal rate (for units on MSU campus): $84/hour + data storage fee
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour + data storage fee
   

We can help design custom probe-based sequence capture targets for studies interested in particular loci or reduced representation genomic sequencing. Below are examples:

• Capture targets from a reference genome assembly. If there is a reference genome closely related to your focal taxa (recommended to not exceed 10% sequence divergence) we can construct optimal, specific sequence targets directly from the genome. If necessary, we would annotate the genome.
• Transcriptome-enabled exome capture. We can design a set of target sequences for exome sequencing from transcriptomes.
• Internal rate (for units on MSU campus): $84/hour + data storage fee
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour + data storage fee

We are happy to work with researchers to provide analyses not included in the above pipelines. This includes generating custom pipelines.

• Internal rate (for units on MSU campus): $84/hour + data storage fee
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour + data storage fee
• Expect custom data analyses to take a minimum of 8 consultant hours.

Primary data from nearly all published genomics studies are available in NCBI’s sequence read archive (SRA). Bioinformatics core consultants can implement and run custom workflows integrating these, or any other, publicly available datasets to generate new hypotheses or draw new conclusions. 

• Internal rate (for units on MSU campus): $84/hour + data storage fee
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour + data storage fee
   

Generation of custom, publication ready figures for the above analyses.

• Internal rate (for units on MSU campus): $84/hour + data storage fee
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour + data storage fee

We offer custom analysis training with different levels of support:

Option 1 (Full Service): A consultant builds an entire analysis pipeline and trains the researcher to use it. Cost is either hourly or percent effort depending on the scope of the project. 

• Internal rate (for units on MSU campus): $84/hour.
• External rate (for foundation, non-profit, or non-MSU university partners): $110/hour

Option 2 (Mentored Development): The trainee and consultant will build the analysis pipeline together with dedicated consultant mentorship at 10-20% of their time (4-8 hours/week). 

• Requires a formal agreement outlining timelines and milestones.
• Requires some R or python, bash, and HPCC skills.
• Cost is ~$13k per year for 10% FTE.

Option 3 (Independent with Free Support): A trainee developing a project independently can troubleshoot with a consultant using our free virtual help desk and weekly office hours. See https://bioinformatics.msu.edu/help-desk for more information.