AmpliconHunter2: a SIMD-Accelerated In-Silico PCR Engine
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arXiv
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| Format: | Preprint |
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2025
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| _version_ | 1866908623196651520 |
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| author | Howard-stone, Rye Mandoiu, Ion |
| author_facet | Howard-stone, Rye Mandoiu, Ion |
| contents | 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 model. AHv2 implements a bit-mask IUPAC matcher with AVX2 SIMD acceleration, supports user-specified mismatches and 3' clamp constraints, calls amplicons in all four primer pair orientations (FR/RF/FF/RR), and optionally trims primers and extracts fixed-length flanking barcodes into FASTA headers. The pipeline packs FASTA into 2-bit batches, streams them in 16 MB chunks, writes amplicons to per-thread temp files and concatenates outputs, minimizing peak RSS during amplicon finding. We also summarize updates to the Python reference (AHv1.1).
Availability and Implementation: AmpliconHunter2 is available as a freely available webserver at: https://ah2.uconn.engr.edu and source code is available at: https://github.com/rhowardstone/AmpliconHunter2 under an MIT license. AHv2 was implemented in C; AHv1.1 using Python 3 with Hyperscan.
Contact: rye.howard-stone@uconn.edu |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2511_00170 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | AmpliconHunter2: a SIMD-Accelerated In-Silico PCR Engine Howard-stone, Rye Mandoiu, Ion Genomics 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 model. AHv2 implements a bit-mask IUPAC matcher with AVX2 SIMD acceleration, supports user-specified mismatches and 3' clamp constraints, calls amplicons in all four primer pair orientations (FR/RF/FF/RR), and optionally trims primers and extracts fixed-length flanking barcodes into FASTA headers. The pipeline packs FASTA into 2-bit batches, streams them in 16 MB chunks, writes amplicons to per-thread temp files and concatenates outputs, minimizing peak RSS during amplicon finding. We also summarize updates to the Python reference (AHv1.1). Availability and Implementation: AmpliconHunter2 is available as a freely available webserver at: https://ah2.uconn.engr.edu and source code is available at: https://github.com/rhowardstone/AmpliconHunter2 under an MIT license. AHv2 was implemented in C; AHv1.1 using Python 3 with Hyperscan. Contact: rye.howard-stone@uconn.edu |
| title | AmpliconHunter2: a SIMD-Accelerated In-Silico PCR Engine |
| topic | Genomics |
| url | https://arxiv.org/abs/2511.00170 |