James Ferguson's repositories
SquiggleKit
SquiggleKit: A toolkit for manipulating nanopore signal data
buttery-eel
The buttery eel - a slow5 guppy/dorado basecaller wrapper
deeplexicon
Signal based nanopore RNA demultiplexing with convolutional neural networks
interARTIC
InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..
fast5_fetcher
A tool for fetching nanopore fast5 files after filtering via demultiplexing, alignment, or other, to improve downstream processing efficiency
SARS-CoV-2_GTG
Genomic Tech's COVID sequencing
nanopore_formats
A place to track nanopore formats
nanopore_NCM18
Helpful scripts for working with Oxford Nanopore Sequencing data
Deepbinner
a signal-level demultiplexer for Oxford Nanopore reads
DeepSimulator_benchmark
The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing.
Folder-Structure-Conventions
Folder / directory structure options and naming conventions for software projects
github-cheat-sheet
A list of cool features of Git and GitHub.
HIVE-seq
HIVepsilon-seq - scalable characterisation of intact persistent proviral HIV reservoirs in women
radian
Nanopore direct RNA basecaller
read_until_api
Read Until client library for Nanopore Sequencing
readfish
Read Until scripts
RODAN
A fully convolutional architecture for basecalling nanopore RNA sequencing data
sigknow_read_until_api
A modification of the readfish changes to the ONT base readUntil API
SquiggleKitDocs
Docs: https://psy-fer.github.io/SquiggleKitDocs/ Code: