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

This repo is for the scripts used in preparation of Flongle Actinomycetes paper

The repository contains the source code of the NanoForms server (Czmil et al. NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology. PeerJ, 2022). It is meant to be the source for standalone server installation. https://doi.org/10.7717/peerj.13056

DeepSelecNet is an enhanced deep learning model to perform read classification for selective sequencing.

Run Oxford Nanopore MinION software in Docker containers. Mirror of https://gitlab.com/lapinskim/minion_docker

Wastewater Enterovirus Typing Tool

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

Nextflow Pipeline for Strain Resolution from Long Reads

Detect and phase minor SNVs from long-read sequencing data

Accompanying information to a scientific publication on the assembly of bacterial genomes using Illumina and nanopore sequencing data using Unicylcer.

Customised reporting of ONT pinfish analysis results

Project to simulate simple Oxford Nanopore Technologies RNA signals

This workflow uses Dorado, Samtools, Clair3, WhatHap and Modkit to extract a modification count table containing information for each relevant site.

Nextflow pipeline incorporating the tracm alignment step alone.

Identification of epigenetic sites in MealyBugs using ONT Nanopore Sequencing

Documentation for the https://github.com/JannesSP/read5 repository

Low level bindings and wrapper for slow5lib, an alternative for ONT Nanopore sequencing FAST5 output

A rapid pipeline for targeted ONT monkeypox sequencing

A novel ML-based binary classifier to tell viral and non-viral long reads apart in metagenomic samples.

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