CLI tool for flexible and fast adaptive sampling on ONT sequencers

Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.

Automated data mangement for Oxford Nanopore DNA sequencing instruments

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.

A implication of stringr package to calculate the pattern detection in R using the stringR package for the pacbio and the oxford nanopore reads

a shorter version of the long_read_polyATGC_trimmer after implementing a array recompile and storing the variables while running a subtle part of the recursion.

a shell code getter for genomics alignments for the illumina and long reads from pacbio and the oxfordnanopore

making bcftools filtering easy. bcftools_filter which will allow for the faster filtering of the variant calls according to the allelic depth and the tags using simple to overlap approaches as compare to implementing the regular patterns.

A regular expression based polyATGC trimmer for the long reads or the fastq reads extremely fast and returns a fasta and also a dataframe for the sequence classification

a long read repeat coverage calculator,given an long read file before assembly either direct from the sequencing runs or after the cleaning, it calculates the total amount of the repeat stretches present in the sequencing reads and you can plot them before assembly

Fast and accurate de novo assembler for long reads

Wastewater Enterovirus Typing Tool

Assembly and intrahost/low-frequency variant calling for viral samples

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.

simON-reads ("Simulate Oxford Nanopore Reads") is a simple yet powerful tool to generate fastq files containing MiniON-like long reads

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

A versatile compressor of third generation sequencing reads.