A fully open source biomolecular structure prediction model based on AlphaFold3 with Apple Silicon support

A repository for collecting GPU basecalling stats

A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

Download FASTQ files from SRA or ENA repositories.

A tool for removing redundant genomes from a set of assemblies

post processing of bacterial pangenome gene presence/absence matrices

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.

A review of the developments and breakthroughs in nanopore sequencing technology during the past decade

A website that displays hundreds of R charts with their code

Visualize whole genome alignments as linear maps

A grammar of graphics for comparative genomics

plotting in the terminal

Ultra-fast and memory-efficient (meta-)genome assembler

The ibd-cluster program uses multi-individual identity by descent to cluster haplotypes

Repository for data, code & figures related to the publication: "Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic"

Template and documentation on how to structure bioinformatic componenets of projects

Jaeger is a quick and precise tool for detecting phages in sequence assemblies.

Gene cluster comparison figure generator

quality filtering tool for long reads

Design and efficiency evaluation of genome-wide sgRNA libraries for CRISPRi-seq

Sequencing and analysis of crAssphage regions from around the globe

compacted de Bruijn graph construction in low memory

Extend hypothetical prokka protein annotations using additional homology searches against larger databases

MMseqs2: ultra fast and sensitive search and clustering suite

De novo assembler for single molecule sequencing reads using repeat graphs

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