3 papers
q-bio.GN2025
AmpliconHunter2: a SIMD-Accelerated In-Silico PCR Engine
Rye Howard-stone, Ion Mandoiu
Summary: We present AmpliconHunter2 (AHv2), a highly scalable in silico PCR engine written in C that can handle degenerate primers and uses a highly accurate melting temperature mo…
q-bio.GN2025
AmpliconHunter: A Scalable Tool for PCR Amplicon Prediction from Microbiome Samples
Rye Howard-Stone, Ion Mandiou
Sequencing of PCR amplicons generated using degenerate primers (typically targeting a region of the 16S ribosomal gene) is widely used in metagenomics to profile the taxonomic comp…
q-bio.GN2025
MHASS: Microbiome HiFi Amplicon Sequencing Simulator
Rye Howard-Stone, Ion Mandoiu
Summary: Microbiome HiFi Amplicon Sequence Simulator (MHASS) creates realistic synthetic PacBio HiFi amplicon sequencing datasets for microbiome studies, by integrating genome-awar…