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Sensitive long-read amplicon sequence variant recovery with savont

Shaw, J.; Riisgaard-Jensen, M.; Andersen, K. S.; Kirkegaard, R.; Dueholm, M. K. D.; Li, H.

2026-05-29 bioinformatics
10.64898/2026.05.26.727271 bioRxiv
Show 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.

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