James Ferguson

kuva. A scientific plotting library in Rust

SquiggleKit. SquiggleKit: A toolkit for manipulating nanopore signal data

blue-crab. lossless nanopore pod5 <=> s/blow5 file conversion

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..

bedpull. bedpull - Pull the query sequence from bam or fasta references using a bed file

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

CoVarPlot. CoVarPlot - Covarage Variant Plots for viral whole genome sequencing

bioinf_tools. Quick and dirty scripts used in my bioinformatics adventures

misc. Various scripts and how-to's related to bioinformatics, genomics, and nanopore sequencing

DeepSimulator_benchmark. The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing.

pysigfish. sigfish python tools

bonito. A PyTorch Basecaller for Oxford Nanopore Reads

gpu-basecalling-benchmarks. GPU basecalling benchmarks and other relevant data

HIVE-seq. HIVepsilon-seq - scalable characterisation of intact persistent proviral HIV reservoirs in women