ClairS - a deep-learning method for long-read somatic small variant calling

SneakySnake:snake: is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.o…

Better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads.

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

🍶 Genome assembly with short sequence reads

VStrains is a de novo approach for reconstructing strains from viral quasispecies.

A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.

Genotyping of segregating mobile elements insertions

FQSqueezer - FASTQ compressor based on k-mer statistics

A scalable variant calling and benchmarking framework supporting both short and long reads.

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

GateSeeder is the first near-memory CPU-FPGA co-design for alleviating both the compute-bound and memory-bound bottlenecks in short and long-read mapping. GateSeeder outperforms Minimap2 by up to 40.3×, 4.8×, and 2.3× when mapping real ONT, HiFi, and Illumina reads, respectively.

Targeted Assembly of Short Reads

Protal is tool for taxonomic profiling from whole-genome shotgun sequencing data. With GTDB marker genes as reference, protal is able to cover most described bacteria. Protal is further able to disentangle intraspecific variation across samples.

Prediction of anti-fungal proteins using protein language models

Evolutionary genomics of chromosomal inversions in Atlantic herring

De novo assembly of SARS-CoV-2 genome

A scalable Nextflow pipeline for automated WGS analysis, optimized for Oxford Nanopore and hybrid ONT–Illumina assemblies in clinical microbiology research.

This project contains a pipeline to analyze raw ancient data, obtained from the sequencing facility. The pipeline includes various Snakemake workflows to process, analyze, and generate reports on the sequence quality, which helps decide if an aDNA extraction and sequencing was successful, and further polishes the data for downstream analyses.

Short read mapping and variant calling