FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2898814350> ?p ?o ?g. }

• W2898814350 abstract "Abstract The analysis of information rich whole-metagenome datasets acquired from complex microbial communities is often restricted by the fragmented nature of assembly from short-read sequencing. The availability of long-reads from third-generation sequencing technologies (e.g. PacBio or Oxford Nanopore) can help improve assembly quality in principle, but high error rates and low throughput have limited their application in metagenomics. In this work, we describe the first hybrid metagenomic assembler which combines the advantages of short and long-read technologies, providing an order of magnitude improvement in contiguity compared to short read assemblies, and high base-pair level accuracy. The proposed approach (OPERA-MS) integrates a novel assembly-based metagenome clustering technique with an exact scaffolding algorithm that can efficiently assemble repeat rich sequences. Based on evaluations with defined in vitro communities and virtual gut microbiomes, we show that it is possible to assemble near complete genomes from metagenomes with as little as 9× long read coverage, thus enabling high quality assembly of lowly abundant species (<1%). Furthermore, OPERA-MS’s fine-grained clustering is able to deconvolute and assemble multiple genomes of the same species in a single sample, allowing us to study the complex dynamics of the human microbiome at the sub-species level. Applying nanopore sequencing to gut metagenomes of patients undergoing antibiotic treatment, we show that long reads can be obtained from stool samples in clinical studies to produce more meaningful metagenomic assemblies (up to 200× improvement over short-read assemblies), including the closed assembly of >80 putative plasmid/phage sequences and a 263kbp jumbo phage. Our results highlight that high-quality hybrid assemblies provide an unprecedented view of the gut resistome in these patients, including strain dynamics and identification of novel plasmid sequences." @default.
• W2898814350 created "2018-11-09" @default.
• W2898814350 creator A5000633958 @default.
• W2898814350 creator A5010636432 @default.
• W2898814350 creator A5016545803 @default.
• W2898814350 creator A5020084026 @default.
• W2898814350 creator A5029982674 @default.
• W2898814350 creator A5037736777 @default.
• W2898814350 creator A5045763170 @default.
• W2898814350 creator A5045792186 @default.
• W2898814350 creator A5059372696 @default.
• W2898814350 creator A5062774997 @default.
• W2898814350 creator A5063112148 @default.
• W2898814350 creator A5064119476 @default.
• W2898814350 creator A5064144504 @default.
• W2898814350 creator A5065881996 @default.
• W2898814350 creator A5074928413 @default.
• W2898814350 creator A5085054240 @default.
• W2898814350 date "2018-10-30" @default.
• W2898814350 modified "2023-10-16" @default.
• W2898814350 title "Nanopore sequencing enables high-resolution analysis of resistance determinants and mobile elements in the human gut microbiome" @default.
• W2898814350 cites W1433995531 @default.
• W2898814350 cites W1703384511 @default.
• W2898814350 cites W1833371888 @default.
• W2898814350 cites W1878521557 @default.
• W2898814350 cites W1902535075 @default.
• W2898814350 cites W1991402127 @default.
• W2898814350 cites W2001561488 @default.
• W2898814350 cites W2004548026 @default.
• W2898814350 cites W2011487263 @default.
• W2898814350 cites W2014268383 @default.
• W2898814350 cites W2016271868 @default.
• W2898814350 cites W2028892116 @default.
• W2898814350 cites W2033617629 @default.
• W2898814350 cites W2041561663 @default.
• W2898814350 cites W2089734397 @default.
• W2898814350 cites W2091826868 @default.
• W2898814350 cites W2093401639 @default.
• W2898814350 cites W2103901746 @default.
• W2898814350 cites W2107282968 @default.
• W2898814350 cites W2108893650 @default.
• W2898814350 cites W2111211467 @default.
• W2898814350 cites W2112203749 @default.
• W2898814350 cites W2112364185 @default.
• W2898814350 cites W2113679889 @default.
• W2898814350 cites W2118688136 @default.
• W2898814350 cites W2129531883 @default.
• W2898814350 cites W2132926880 @default.
• W2898814350 cites W2133579817 @default.
• W2898814350 cites W2137759177 @default.
• W2898814350 cites W2141040548 @default.
• W2898814350 cites W2141202455 @default.
• W2898814350 cites W2141920662 @default.
• W2898814350 cites W2157888653 @default.
• W2898814350 cites W2160969485 @default.
• W2898814350 cites W2167952120 @default.
• W2898814350 cites W2175526948 @default.
• W2898814350 cites W2179507357 @default.
• W2898814350 cites W2263818957 @default.
• W2898814350 cites W2264290069 @default.
• W2898814350 cites W2270324082 @default.
• W2898814350 cites W2294353708 @default.
• W2898814350 cites W2337261418 @default.
• W2898814350 cites W2345730070 @default.
• W2898814350 cites W2383775397 @default.
• W2898814350 cites W2509730012 @default.
• W2898814350 cites W2559838906 @default.
• W2898814350 cites W2575750030 @default.
• W2898814350 cites W2587091458 @default.
• W2898814350 cites W2587678577 @default.
• W2898814350 cites W2597036303 @default.
• W2898814350 cites W2599417231 @default.
• W2898814350 cites W2607669908 @default.
• W2898814350 cites W2610214149 @default.
• W2898814350 cites W2610769220 @default.
• W2898814350 cites W2730233141 @default.
• W2898814350 cites W2736920791 @default.
• W2898814350 cites W2741628575 @default.
• W2898814350 cites W2760526698 @default.
• W2898814350 cites W2767898240 @default.
• W2898814350 cites W2769228004 @default.
• W2898814350 cites W2773939681 @default.
• W2898814350 cites W2800650583 @default.
• W2898814350 cites W2808098636 @default.
• W2898814350 cites W2950150251 @default.
• W2898814350 cites W2950354111 @default.
• W2898814350 cites W2952167528 @default.
• W2898814350 cites W2952689752 @default.
• W2898814350 cites W4236236547 @default.
• W2898814350 doi "https://doi.org/10.1101/456905" @default.
• W2898814350 hasPublicationYear "2018" @default.
• W2898814350 type Work @default.
• W2898814350 sameAs 2898814350 @default.
• W2898814350 citedByCount "12" @default.
• W2898814350 countsByYear W28988143502018 @default.
• W2898814350 countsByYear W28988143502019 @default.
• W2898814350 countsByYear W28988143502020 @default.
• W2898814350 countsByYear W28988143502021 @default.
• W2898814350 countsByYear W28988143502022 @default.
• W2898814350 crossrefType "posted-content" @default.

• next