Slides/notes and Jupyter notebook demos for an introductory course of numerical analysis/scientific computing

GeneMark-ETP: gene finding in eukaryotic genomes supported by transcriptome sequencing and protein homology

User-friendly Scheduler for sub-node tasks for HPC systems

A safe wrapper for [m,c,re]alloc/free functions =)

Posit Cheat Sheets - Can also be found at https://posit.co/resources/cheatsheets/.

GFA visualizer, GPU-accelerated using Vulkan

GFA parser in Rust

Collection of bioinformatics training materials

Adds SEQ and QUAL to secondary alignments from SAM/BAM/CRAM

Align proteins to genomes with splicing and frameshift

Draw Newick format phylogenetic trees.

Range-based for loops to iterate over a range of numbers or values

Population genetics notes

A 21st century LaTeX wrapper

A visual editor for research.

Reviews for the Journal of Open Source Software

NovoGraph: building whole genome graphs from long-read-based de novo assemblies

Kmer-guided processing of jumping reads

R-script for generating canonical diagrams of distributions to be used to describe Bayesian hierarchical models.

NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. This allows …

A program for the Maximum-likelihood analysis of population genomic data.

Standalone C library for assembling Illumina short reads in small regions

Embeddable genomic visualization component based on the Integrative Genomics Viewer

Interactive in-browser track viewer

discoal is a coalescent simulation program capable of simulating models with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples

MrBayes script used for the gene content analysis of Pisani et al. 2015

Scalable gVCF merging and joint variant calling for population sequencing projects