rchapman2000,Ryan Chapman,github

Hi there 👋

My name is Ryan Chapman, and I am an incoming medical student at University of Nebraska Medical Center! I completed my Bachelor of Science in Bioinformatics at the University of Nebraska at Omaha in July of 2023, and my background is in Infectious Diseases.

My past positions include:

Bioinformatician in the Laboratory of Dr. Michael Wiley at the University of Nebraska Medical Center (June 2022 - June 2023)
Bioinformatician for PraesensBio LLC (October 2022 - June 2023)
Undergraduate Research Assistant in the Laboratory of Dr. Paul Davis at the University of Nebraska at Omaha (October 2019 - May 2023)

My past work includes:

Reference Based and De Novo assembly of viral pathogens
NGS Analysis Automation with Nextflow
SARS-CoV-2 Wastewater Detection and Characterization
Viral Phylogenetics
Library Preparation and Analysis of Illumina and Oxford Nanopore sequencing data.
Transcriptomic analyses (including Bulk and Single-Cell RNA-Seq)
Identification of genomic repeat regions for potential PCR diagnostics

I have several NGS Assembly Pipelines published that you are free to use! Please let me know if you discover any Issues/Bugs!

Ryan Chapman's Projects

amplify

AmpLify is an automated amplicon sequencing analysis pipeline built for SWIFT Biosciences products

artic-ncov-wrapper

A wrapper script to automated the artic-ncov script

consensus-variant-annotation-pipeline

A nextflow pipeline that automates the process of comparing a consensus genome to a given reference and identifying/annotating variant positions.

covid-wastewater-ne

Scripts and tests relating to the processing and visualization of SARS-CoV-2 lineage abundances from Nebraska

de-novo-reference-correction-pipeline

A nextflow pipeline that assembles a genome by first performing a de novo assembly, using the de novo assembly to correct a reference genome, and finally performing a reference-based assembly to that corrected reference.