Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing
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Title
Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing
Authors
Keywords
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Journal
NATURE METHODS
Volume 19, Issue 7, Pages 823-826
Publisher
Springer Science and Business Media LLC
Online
2022-07-05
DOI
10.1038/s41592-022-01539-7
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- Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
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- Scaling laws predict global microbial diversity
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