rchapman2000
Bioinformatician | Infectious Diseases | Incoming Medical Student | Coffee Addict
University of Nebraska Medical CenterNebraska, USA
Pinned Repositories
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
covid_swift_pipeline
de-novo-assembly-pipeline
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.
ont-de-novo-assembly
A de novo assembly pipeline for sequencing data using Oxford Nanopore Technologies
ont-ref-based-assembly
A reference-based assembly pipeline designed for analysis of Oxford Nanopore sequencing data
ref-based-assembly-pipeline
rchapman2000's Repositories
rchapman2000/ont-ref-based-assembly
A reference-based assembly pipeline designed for analysis of Oxford Nanopore sequencing data
rchapman2000/AmpLify
AmpLify is an automated amplicon sequencing analysis pipeline built for SWIFT Biosciences products
rchapman2000/de-novo-assembly-pipeline
rchapman2000/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.
rchapman2000/ont-de-novo-assembly
A de novo assembly pipeline for sequencing data using Oxford Nanopore Technologies
rchapman2000/ref-based-assembly-pipeline
rchapman2000/artic-ncov-wrapper
A wrapper script to automated the artic-ncov script
rchapman2000/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.
rchapman2000/COVID-WasteWater-NE
Scripts and tests relating to the processing and visualization of SARS-CoV-2 lineage abundances from Nebraska
rchapman2000/covid_swift_pipeline
rchapman2000/Ghana-2022-Marburg-Phylogenetics
Phylogenetic Analysis of Marburg Virus Genomes Sequenced in Ghana - August 2022
rchapman2000/NCBI-Genome-Download
A python script to automate the process of downloading organism genomes and metadata from NCBI
rchapman2000/ont-influenza-typing
A pipeline to type influenza reads produced by Oxford Nanopore Sequencing
rchapman2000/xgen-ont-pipeline
Assembles genomes from IDT's xGen amplicon sequencing data processed on Oxford Nanopore Sequencing Technology
rchapman2000/hello-world
The age-old programming tradition!
rchapman2000/rchapman2000