Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling

✏️ Genome assembly polishing & SNV detection

VirusWarn-SC2 is a simple Variants of concern aLert system script for SARS-CoV-2.

A mutation-based alert system to prioritize concerning Influenza variants from sequencing data.

Comprehensive Sanger sequence analysis and clinical reporting tool. Identifies SNVs and Indels precisely while keeping your genetic data secure locally.

Korai is a project used to detect variants in malware samples using a created phylogenetic tree. The project is named as the antagonist to Mirai, its focus malware family. Mirai stands for "the Future", while Korai represents "the Past" as we look at old samples and their evolution to see the (variants of) Mirai.

Optimized Python and C++ implementations of INDELseek, a Perl tool for detecting complex genetic indels in NGS data, with performance improvements, validation, and benchmarking against other variant callers.

R package for entropy-informed detection of emerging viral variants and genomic surveillance. Implements per-site Shannon entropy, Gaussian mixture model site selection, Hellinger distance, and non-parametric change-point detection. Validated on SARS-CoV-2 Spike protein sequences from NCBI and GISAID databases.

Lab module and lectures for variant detection in SARS-CoV-2 using Galaxy