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…

🍶 Genome assembly with short sequence reads

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

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

Genotyping of segregating mobile elements insertions

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

FQSqueezer - FASTQ compressor based on k-mer statistics

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

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

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.

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

Targeted Assembly of Short Reads

TAIFA is a workflow for conducting Whole-Genome Sequencing (WGS) of bacteria

Evolutionary genomics of chromosomal inversions in Atlantic herring

Short read mapping and variant calling

Synthetically Engineered Wastewater sequence data for Assessing Genomic Entities

A flexible complex genome rearrangement simulator for short and long reads

Nextflow pipeline for short-read alignment

A nextflow pipeline to calculate depth of coverage from a metagenomic set of bins