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
An extension to the wavefront algorithm that generalizes it to work on directed acyclic sequence graphs
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
[RECOMB-seq '25] Code repository for the paper "Efficient Trace Reconstruction for DNA Data Storage Systems using Bidirectional Beam Search"
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.
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.
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