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.

Genotyping of segregating mobile elements insertions

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

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

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

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

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

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

A flexible complex genome rearrangement simulator for short and long reads

Nextflow pipeline for short-read alignment

Synthetically Engineered Wastewater sequence data for Assessing Genomic Entities

A sequence-read simulator program for NGS