abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.

ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to amalgamate reads derived from the same DNA template into a consensus sequence.

Detecting transposable element invasions without repeat library. Detects also horizontal transfer events and endogenized viruses. All you need is a reference genome and some short reads

ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome

An extension to the wavefront algorithm that generalizes it to work on directed acyclic sequence graphs

SARS2seq is a pipeline designed to process raw FastQ data from targeted SARS-CoV-2 sequencing and generate biologically correct consensus sequences of the SARS-CoV-2 genome.

[RECOMB-seq '25] Code repository for the paper "Efficient Trace Reconstruction for DNA Data Storage Systems using Bidirectional Beam Search"

Avalanche Consensus is a consensus protocol that is scalable, robust, and decentralized. It combines features of both classical and Nakamoto consensus mechanisms to achieve high throughput, fast finality, and energy efficiency

SARS-CoV-2 sequencing workflow

Align SARS-CoV-2 sequences against a reference genome, and trim UTR sequences

Tools for analyzing LINE-1 elements

Zero-knowledge proof (ZKP) implementation for viral consequence sequence generation.