Project to simulate simple Oxford Nanopore Technologies RNA signals
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Updated
May 15, 2024 - Python
Project to simulate simple Oxford Nanopore Technologies RNA signals
Automated data mangement for Oxford Nanopore DNA sequencing instruments
Quality control plotting for long reads
Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
⛏ HLA predictions from NGS shotgun data
Assembly and intrahost/low-frequency variant calling for viral samples
Fast and accurate de novo assembler for long reads
CLI tool for flexible and fast adaptive sampling on ONT sequencers
Marcus Viscardi's personal scripts used to analyze outputs of dRNA seq w/ ONT. Please feel free to reach out if you are interested in utilizing any of this code!
This page is contains all the software and commands I've used for my mtDNA analysis.
pattern detection in R using the stringR package for the pacbio and the oxford nanopore reads
long_read_polyATGC_trimmer using regular expression.
code getter for illumina, pacbio, oxford long reads alignments.
bcftools for dealing with bcf files.
polyATGC pacbio or oxford nanopore long reads trimmer.
pacbio or oxford nanopore long reads repeat coverage estimation.
Wastewater Enterovirus Typing Tool
A rapid pipeline for targeted ONT monkeypox sequencing
Long read based human genomic structural variation detection with cuteSV
A novel ML-based binary classifier to tell viral and non-viral long reads apart in metagenomic samples.
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