Draw RNA secondary structures in python.

[WORK IN PROGRESS]: Pysam2 is a module for Python 3.6 or newer for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib v2 C-API, the same one that powers samtoo…

Methylation/modified base calling separated from basecalling.

Tools (written in C using htslib) for manipulating next-generation sequencing data

Long read / genome alignment software

Identification of differential RNA modifications from nanopore direct RNA sequencing

Simple utility to concatenate .fastq(.gz) files whilst creating a summary of the sequences.

Command line directory bookmarks with jumping to bookmarks, subdirectory tab completion, distant listing etc

Linear mixed model for genomic analyses.

ENA upload cli - script your Open Data upload to the European Nucleotide Archive

What the f*ck Python? 😱

Tensors and Dynamic neural networks in Python with strong GPU acceleration

Create an argparse.ArgumentParser from function docstrings

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network out…

SIRVsuite is a command line tool to QC an RNA-Seq workflow using Lexogen's SIRV spike-in controls.

Methylation Phasing for Nanopore Sequencing

Drawings / tilings / patterns generally written in PostScript

CLI tool for flexible and fast adaptive sampling on ONT sequencers

Pairwise Sequence Alignment Library

Convert SAM/BAM files with transcript coordinates to SAM files with genomic coordinates

Snakemake profile for running jobs on an LSF cluster

A colored formatter for the python logging module

Template for the web slides - reveal.js

HDF5-based container format for Methylation calls from long reads

Clone me to create your Manubot manuscript

the pangenome graph builder

Pangenome Graph Variation Format (PGVF)

Long-read splice alignment with high accuracy