Pan-genomic Matching Statistics for Targeted Nanopore Sequencing

Ahmed, Omar, Rossi, Massimiliano, Kovaka, Sam, Schatz, Michael C, Gagie, Travis, Boucher, Christina, Langmead, Ben (June 2021) Pan-genomic Matching Statistics for Targeted Nanopore Sequencing. iScience. p. 102696. ISSN 2589-0042

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Abstract

Nanopore 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.

Item Type:	Paper
Subjects:	bioinformatics > genomics and proteomics > analysis and processing > Sequence Data Processing bioinformatics > computational biology
CSHL Authors:	Schatz, Michael C.
Communities:	CSHL labs > Schatz lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	June 2021
Date Deposited:	29 Jun 2021 18:33
Last Modified:	15 Nov 2023 18:46
PMCID:	PMC8237286
URI:	https://repository.cshl.edu/id/eprint/40236

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