Bioinformatics

We offer a wide range of bioinformatic and data analysis services, billed hourly. Ideally, we prefer if you discuss with us at the beginning stages of your experiment so we can consult about planning and design; however, we can help at any stage. You may contact our bioinformatician, Jake Szamosi to get started.

Initial consultations are always free. It gives you a chance to explain your scientific inquiry and your budget, so that we can provide you with a plan and an estimate. We will continue to keep you updated if complications arise that will affect the cost of our service. We use open-source analysis software wherever possible and always provide clients with all code or scripts used to run the analysis, to make replication easier. A brief methods and results write-up that can be included or adapted for publication will also be included.

The most common services we offer include:

Genomics

  • draft viral or prokaryotic genome assembly
  • variant calling
  • SNP analysis
  • multiple genome alignment
  • complicated comparative genomic projects

RNASeq

  • prokaryotic differential expression analysis (bwa, HTSeq, DESeq)
  • eukaryotic differential expression (STAR, JunctionSeq, DESeq)
  • splice junction analysis (STAR, JunctionSeq, DESeq)

16S Microbiome

  • 16S marker gene microbiome analysis (including taxa bar charts, alpha and beta diversity analysis, differential abundance analysis, or more complicated analyses using unsupervised clustering or co-occurrence analysis)

Please contact us if you are interested in an analysis that is not mentioned here. Chances are good that we can help.

 

Service Cost

The cost of these services will vary depending on factors such as how complicated the scientific question is, the quality of the data, whether standard tools exist or if methods need to be developed. Here are some examples with likely time estimates:

Draft bacterial genome assembly (straightforward): 2—5 hours

RNASeq differential expression analysis with two or three groups: 3 – 6 hours

16S analysis* (straightforward) including taxa bar charts, alpha and beta diversity, and DESeq analysis of differential abundance: 5 – 15 hours

*16S analyses, especially of human data, can often turn out to be quite complicated, and the number of hours can grow if your experiment has low n, includes many confounding factors, or if you are interested in different kinds of analyses.

 

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