摘要：SummaryNanopore sequencing is an increasingly powerful tool for genomics. Recently, computational advances have allowed nanopores to sequence in a targeted fashion; as the sequencer emits data, software can analyze the data in real time and signal the sequencer to eject “nontarget” DNA molecules. We present a novel method called SPUMONI, which enables rapid and accurate targeted sequencing using efficient pan-genome indexes. SPUMONI uses a compressed index to rapidly generate exact or approximate matching statistics in a streaming fashion. When used to target a specific strain in a mock community, SPUMONI has similar accuracy as minimap2 when both are run against an index containing many strains per species. However SPUMONI is 12 times faster than minimap2. SPUMONI's index and peak memory footprint are also 16 to 4 times smaller than those of minimap2, respectively. This could enable accurate targeted sequencing even when the targeted strains have not necessarily been sequenced or assembled previously.Graphical abstractDisplay OmittedHighlights•SPUMONI uses an efficient pan-genome index to eject nontarget reads from the nanopore•Read classifications are highly accurate for typical nanopore sequencing error rates•For larger pan-genomes, SPUMONI is faster and uses less memory than minimap2•Enables analyses for strains that are missing or poorly represented in databasesGenomics; Biotechnology; Bioinformatics; Biocomputational method
