Precision Medicine

Precision Medicine

Expression Analysis in RNASeq

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This workflow can be used to determine gene expression, splice variants and differential expression analysis.

Version 1.1.1

Use Cases

  • Determine differentially expressed genes between two or more groups of samples (treated vs untreated, knock-out vs wildtype, cell type A vs cell type B)
  • Determine differentially expressed transcripts between two or more groups of samples
  • Compare the gene expression profiles of samples

Summary and Methods

This workflow is designed to help the user thoroughly analyze RNA sequencing data. Currently, two functions are supported: Full Analysis and Recalculate Statistics. Both functions include the option to specify whether the data include Human Cancer Samples. Click the toggles below to learn more about each function.

Full Analysis

Recalculate Statistics

Human Cancer

Inputs

Outputs

Workflow Walkthrough

Results Walkthrough

Citations

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Genomic Variant Analysis

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Identify single-nucleotide variants (SNVs), indels, and structural variants in a diploid genome resequencing projects by comparison to a reference genome.

Version 1.6.1

Use Cases

  • Determine variants in DNA samples compared to a reference genome including single nucleotide variants (SNVs), insertions, deletions and structural variants
    • Germline Variant Calling
    • Variant Calling in Ancient DNA
    • Somatic Mutation Detection
  • Determine variants in DNA samples compared to a custom reference genome for small or synthetic genomes
    • Plasmid
    • Virus
    • Bacteria
    • Synthetic Genome
  • Sequencing Platform supported include Illumina, Pacbio and Oxford Nanopore (ONT)

Summary and Methods

This workflow is designed to help the user determine variants in DNA samples when compared to a reference genome. Currently, four different input DNA datatypes are supported: Germline (Diploid)Ancient DNASmall Genomes (Viral/Prokaryotic/Synthetic), and Somatic (Human Cancer). Workflows can be run either with Parabricks, Sentieon or native open-source tools (NOST). Click the toggles below to learn more about each supported dataype.

Germline (Diploid)

Ancient DNA

Small Genomes (Viral/Prokaryotic/Synthetic)

Somatic (Human Cancer)

Inputs

Outputs

Workflow Walkthrough

Results Walkthrough

Citations

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Human Haplotype

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Determine the haplotype of certain human genes, include HLA, RBG, and Codis.

Version 0.0.2

Summary

Sequence reads are aligned and their haplotype is predicted using Hisat-Genotype [1].

Workflow Walkthrough

Citations

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