Sensitive long-read amplicon sequence variant recovery with savont
Abstract
Abstract Long-read amplicon sequencing can profile longer sequences compared to short reads, but recovering amplicon sequence variants (ASVs) is a challenge for long, noisy reads. We present savont, an algorithm for recovering ASVs from modern long-read amplicons with mean accuracy ≥ 98%, including Oxford Nanopore Technologies (ONT) R10.4 and PacBio HiFi reads. Savont requires 5 to 16 times lower sequencing depth for full-length 16S rRNA ONT reads than previous methods and generates up to 95 times more ASVs for complex environments. Savont makes ASV-based analysis from shallow and noisy long-read amplicon sequencing feasible.
Fields of Study & Subjects
Genomics and Phylogenetic Studies
Genomic variations and chromosomal abnormalities
Genomics and Rare Diseases
Publication details
- Journal / source
- bioRxiv (Cold Spring Harbor Laboratory)
- Publisher
- openRxiv
- Publication date
- 29 May 2026
- Language
- EN
- Document type
- Preprint