JupyterLab desktop application, based on Electron.

updated vsgseq pipeline

Script to split and map Oxford Nanopore reads for VSG-BarSeq experiments.

python module to plot beautiful and highly customizable genome browser tracks

Comparison of multiple long read datasets

A single molecule sequence assembler for genomes large and small.

Software for detecting regions of BrdU and EdU incorporation in Oxford Nanopore reads.

VSG analysis pipeline

Nanopore data assembler

A genome annotation tool for more than just protists

A PyTorch Basecaller for Oxford Nanopore Reads

Methylation/modified base calling separated from basecalling.

pycoSnake is a neatly wrapped collection of snakemake workflows for analysing nanopore and Illumina sequencing data

RNA modifications detection from Nanopore dRNA-Seq data

Magnipore: Differential single nucleotide changes of ONT signals

Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)

DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using Nanopore direct RNA sequencing

De novo assembly from Oxford Nanopore reads.

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

De novo assembler for single molecule sequencing reads using repeat graphs

Splitting of sequence reads by internal adapter sequence search

Variant Antigen Profiling for Trypanosoma congolense and Trypanosoma vivax

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

Grid and ggplot2 based visualization for biological data

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

🌺 reference-free transcriptome assembly for short and long reads

COVERnant - A tool to generate and manipulate coverage plots of high-throughput sequencing data.

SRA Tools

Official code repository for GATK versions 4 and up