Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs.

Abstract:

:Assembly of metagenomic samples is a very complex process, with algorithms designed to address sequencing platform-specific issues, (read length, data volume, and/or community complexity), while also faced with genomes that differ greatly in nucleotide compositional biases and in abundance. To address these issues, we have developed a post-assembly process: MetaGenomic Assembly by Merging (MeGAMerge). We compare this process to the performance of several assemblers, using both real, and in-silico generated samples of different community composition and complexity. MeGAMerge consistently outperforms individual assembly methods, producing larger contigs with an increased number of predicted genes, without replication of data. MeGAMerge contigs are supported by read mapping and contig alignment data, when using synthetically-derived and real metagenomic data, as well as by gene prediction analyses and similarity searches. MeGAMerge is a flexible method that generates improved metagenome assemblies, with the ability to accommodate upcoming sequencing platforms, as well as present and future assembly algorithms.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Scholz M,Lo CC,Chain PS

doi

10.1038/srep06480

subject

Has Abstract

pub_date

2014-10-01 00:00:00

pages

6480

issn

2045-2322

pii

srep06480

journal_volume

4

pub_type

杂志文章
  • Transcriptome Analysis Reveals Candidate Genes involved in Blister Blight defense in Tea (Camellia sinensis (L) Kuntze).

    abstract::To unravel the molecular mechanism of defense against blister blight (BB) disease caused by an obligate biotrophic fungus, Exobasidium vexans, transcriptome of BB interaction with resistance and susceptible tea genotypes was analysed through RNA-seq using Illumina GAIIx at four different stages during ~20-day disease ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep30412

    authors: Jayaswall K,Mahajan P,Singh G,Parmar R,Seth R,Raina A,Swarnkar MK,Singh AK,Shankar R,Sharma RK

    更新日期:2016-07-28 00:00:00

  • Mutational convergence acts as a major player in adaptive parallel evolution of Shigella spp.

    abstract::Shigella spp., emerging from multiple origins of Escherichia coli, poses a significant health threat as a causative agent of bacillary dysentery. While multiple serotypes of four different species have evolved via independent lineages, Shigella spp. are designated as a single pathotype, primarily because of their comm...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-39810-1

    authors: Thomas AK,Preetha S,Omanakuttan A,Vidyullata L,Ashokan A,Rajachandran V,Chattopadhyay S

    更新日期:2019-03-01 00:00:00

  • Overcoming challenges in human saliva gene expression measurements.

    abstract::Saliva, as a non-invasive and easily accessible biofluid, has been shown to contain RNA biomarkers for prediction and diagnosis of several diseases. However, systematic analysis done by our group identified two problematic issues not coherently described before: (1) most of the isolated RNA originates from the oral mi...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-67825-6

    authors: Ostheim P,Tichý A,Sirak I,Davidkova M,Stastna MM,Kultova G,Paunesku T,Woloschak G,Majewski M,Port M,Abend M

    更新日期:2020-07-07 00:00:00

  • Size distribution of magnetic charge domains in thermally activated but out-of-equilibrium artificial spin ice.

    abstract::A crystal of emerging magnetic charges is expected in the phase diagram of the dipolar kagomé spin ice. An observation of charge crystallites in thermally demagnetized artificial spin ice arrays has been recently reported by S. Zhang and coworkers and explained through the thermodynamics of the system as it approaches...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep05702

    authors: Montaigne F,Lacour D,Chioar IA,Rougemaille N,Louis D,Mc Murtry S,Riahi H,Burgos BS,Menteş TO,Locatelli A,Canals B,Hehn M

    更新日期:2014-07-16 00:00:00

  • Radio-frequency current drive for thermonuclear fusion reactors.

    abstract::Principal research on energy from thermonuclear fusion uses Deuterium-Tritium plasmas magnetically trapped in toroidal devices. As major scientific problem for an economic (i.e., really feasible) reactor, we must understand how to lead strongly heated plasmas to sustain a high fusion gain while large fraction of curre...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-27996-9

    authors: Cardinali A,Castaldo C,Cesario R,Amicucci L,Galli A,Napoli F,Panaccione L,Riccardi C,Santini F,Schettini G,Tuccillo AA

    更新日期:2018-07-09 00:00:00

  • Inferring genetic origins and phenotypic traits of George Bähr, the architect of the Dresden Frauenkirche.

    abstract::For historic individuals, the outward appearance and other phenotypic characteristics remain often non-resolved. Unfortunately, images or detailed written sources are only scarcely available in many cases. Attempts to study historic individuals with genetic data so far focused on hypervariable regions of mitochondrial...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-20180-z

    authors: Peltzer A,Mittnik A,Wang CC,Begg T,Posth C,Nieselt K,Krause J

    更新日期:2018-02-01 00:00:00

  • Sea ice breakup and marine melt of a retreating tidewater outlet glacier in northeast Greenland (81°N).

    abstract::Rising temperatures in the Arctic cause accelerated mass loss from the Greenland Ice Sheet and reduced sea ice cover. Tidewater outlet glaciers represent direct connections between glaciers and the ocean where melt rates at the ice-ocean interface are influenced by ocean temperature and circulation. However, few measu...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-05089-3

    authors: Bendtsen J,Mortensen J,Lennert K,K Ehn J,Boone W,Galindo V,Hu YB,Dmitrenko IA,Kirillov SA,Kjeldsen KK,Kristoffersen Y,G Barber D,Rysgaard S

    更新日期:2017-07-10 00:00:00

  • Piezoelectric extraction of ECG signal.

    abstract::The monitoring and early detection of abnormalities or variations in the cardiac cycle functionality are very critical practices and have significant impact on the prevention of heart diseases and their associated complications. Currently, in the field of biomedical engineering, there is a growing need for devices cap...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep37093

    authors: Ahmad MA

    更新日期:2016-11-17 00:00:00

  • The first two cell-fate decisions of preimplantation mouse embryo development are not functionally independent.

    abstract::During mouse preimplantation embryo development, three distinct cell lineages are formed, represented by the differentiating trophectoderm (TE), primitive endoderm (PrE) and the pluripotent epiblast (EPI). Classically, lineage derivation has been presented as a two-step process whereby outer TE cells are first segrega...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep15034

    authors: Mihajlović AI,Thamodaran V,Bruce AW

    更新日期:2015-10-13 00:00:00

  • Co-fermentation using Recombinant Saccharomyces cerevisiae Yeast Strains Hyper-secreting Different Cellulases for the Production of Cellulosic Bioethanol.

    abstract::To realize the economical production of ethanol and other bio-based chemicals from lignocellulosic biomass by consolidated bioprocessing (CBP), various cellulases from different sources were tested to improve the level of cellulase secretion in the yeast Saccharomyces cerevisiae by screening an optimal translational f...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-04815-1

    authors: Lee CR,Sung BH,Lim KM,Kim MJ,Sohn MJ,Bae JH,Sohn JH

    更新日期:2017-06-30 00:00:00

  • FTY720-induced endocytosis of yeast and human amino acid transporters is preceded by reduction of their inherent activity and TORC1 inhibition.

    abstract::FTY720 is a sphingoid base analog that acts as an anticancer agent in animal models. Its effect on tumor cells stems largely from its ability to trigger endocytosis of several nutrient transporters. The observation that FTY720 similarly stimulates downregulation of amino acid permeases in yeast suggests that the cellu...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-14124-2

    authors: Barthelemy C,Barry AO,Twyffels L,André B

    更新日期:2017-10-23 00:00:00

  • Short range magnetic exchange interaction favors ferroelectricity.

    abstract::Multiferroics, where two or more ferroic order parameters coexist, is one of the hottest fields in condensed matter physics and materials science. To search multiferroics, currently most researches are focused on frustrated magnets, which usually have complicated magnetic structure and low magnetic ordering temperatur...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep22743

    authors: Wan X,Ding HC,Savrasov SY,Duan CG

    更新日期:2016-03-09 00:00:00

  • Do nuclear-encoded core subunits of mitochondrial complex I confer genetic susceptibility to schizophrenia in Han Chinese populations?

    abstract::Schizophrenia is one of the most prevalent psychiatric disorders with complex genetic etiology. Accumulating evidence suggests that energy metabolism and oxidative stress play important roles in the pathophysiology of schizophrenia. Dysfunction of mitochondrial respiratory chain and altered expression of complex I sub...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep11076

    authors: Li X,Zhang W,Tang J,Tan L,Luo XJ,Chen X,Yao YG

    更新日期:2015-06-08 00:00:00

  • Meta-analysis of soil mercury accumulation by vegetables.

    abstract::Mercury pollution in soil poses serious risks to human health through consumption of contaminated vegetables. We used a meta-analysis to examine the mercury enrichment ability of different vegetables and the main factors affecting mercury uptake. We drew the following conclusions. (1) Plants with a lower bioconcentrat...

    journal_title:Scientific reports

    pub_type: 杂志文章,meta分析

    doi:10.1038/s41598-018-19519-3

    authors: Yu H,Li J,Luan Y

    更新日期:2018-01-19 00:00:00

  • High fidelity CRISPR/Cas9 increases precise monoallelic and biallelic editing events in primordial germ cells.

    abstract::Primordial germ cells (PGCs), the embryonic precursors of the sperm and egg, are used for the introduction of genetic modifications into avian genome. Introduction of small defined sequences using genome editing has not been demonstrated in bird species. Here, we compared oligonucleotide-mediated HDR using wild type S...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-33244-x

    authors: Idoko-Akoh A,Taylor L,Sang HM,McGrew MJ

    更新日期:2018-10-11 00:00:00

  • Hyperspectral near infrared imaging quantifies the heterogeneity of carbon materials.

    abstract::For many applications heterogeneity is a direct indicator of material quality. Reliable determination of chemical heterogeneity is however not a trivial task. Spectral imaging can be used for determining the spatial distribution of an analyte in a sample, thus transforming each pixel of an image into a sampling cell. ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-28889-7

    authors: Mäkelä M,Geladi P

    更新日期:2018-07-11 00:00:00

  • Long-term bowel dysfunction following low anterior resection.

    abstract::Study aimed to assess long-term bowel function in patients who underwent low anterior resection for cancer five and more years ago. Patients who underwent low anterior resection for rectal cancer from 2010 to 2015 at National Cancer Institute were prospectively included in our study. They were interviewed using low an...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-68900-8

    authors: Dulskas A,Kavaliauskas P,Pilipavicius L,Jodinskas M,Mikalonis M,Samalavicius NE

    更新日期:2020-07-17 00:00:00

  • Possible existence of optical communication channels in the brain.

    abstract::Given that many fundamental questions in neuroscience are still open, it seems pertinent to explore whether the brain might use other physical modalities than the ones that have been discovered so far. In particular it is well established that neurons can emit photons, which prompts the question whether these biophoto...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep36508

    authors: Kumar S,Boone K,Tuszyński J,Barclay P,Simon C

    更新日期:2016-11-07 00:00:00

  • Renal Prognosis and Related Risk Factors for Henoch-Schönlein Purpura Nephritis: A Chinese Adult Patient Cohort.

    abstract::This study investigated the clinicopathological characteristics of Henoch-Schönlein purpura nephritis (HSPN) in Chinese adult patients and analyzed the renal outcomes and prognostic risk factors for progression to end-stage renal disease (ESRD). Adult patients who had biopsy-proven HSPN were studied. Their clinicopath...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-23638-2

    authors: Huang X,Wu X,Le W,Hao Y,Wu J,Zeng C,Liu Z,Tang Z

    更新日期:2018-04-03 00:00:00

  • A Probabilistic Model for Estimating the Depth and Threshold Temperature of C-fiber Nociceptors.

    abstract::The subjective experience of thermal pain follows the detection and encoding of noxious stimuli by primary afferent neurons called nociceptors. However, nociceptor morphology has been hard to access and the mechanisms of signal transduction remain unresolved. In order to understand how heat transducers in nociceptors ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep17670

    authors: Dezhdar T,Moshourab RA,Fründ I,Lewin GR,Schmuker M

    更新日期:2015-12-07 00:00:00

  • Neutral poly-/perfluoroalkyl substances in air and snow from the Arctic.

    abstract::Levels of neutral poly-/perfluoroalkyl substances (nPFASs) in air and snow collected from Ny-Ålesund were measured and their air-snow exchange was determined to investigate whether they could re-volatilize into the atmosphere driven by means of air-snow exchange. The total concentration of 12 neutral PFASs ranged from...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep08912

    authors: Xie Z,Wang Z,Mi W,Möller A,Wolschke H,Ebinghaus R

    更新日期:2015-03-09 00:00:00

  • Creation of vortices by torque in multidimensional media with inhomogeneous defocusing nonlinearity.

    abstract::Recently, a new class of nonlinear systems was introduced, in which the self-trapping of fundamental and vortical localized modes in space of dimension D is supported by cubic self-repulsion with a strength growing as a function of the distance from the center, r, at any rate faster that r(D). These systems support ro...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep09420

    authors: Driben R,Meier T,Malomed BA

    更新日期:2015-03-24 00:00:00

  • Learning a Health Knowledge Graph from Electronic Medical Records.

    abstract::Demand for clinical decision support systems in medicine and self-diagnostic symptom checkers has substantially increased in recent years. Existing platforms rely on knowledge bases manually compiled through a labor-intensive process or automatically derived using simple pairwise statistics. This study explored an aut...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-05778-z

    authors: Rotmensch M,Halpern Y,Tlimat A,Horng S,Sontag D

    更新日期:2017-07-20 00:00:00

  • The relationship between altered mitochondrial DNA copy number and cancer risk: a meta-analysis.

    abstract::Currently, a comprehensive assessment between mitochondrial DNA (mtDNA) content and cancer risk is lacking. We designed this meta-analysis to test the hypothesis that altered mtDNA copy number might influence genetic susceptibility to some specific types of cancer. The processes of literature search, eligibility appra...

    journal_title:Scientific reports

    pub_type: 杂志文章,meta分析

    doi:10.1038/srep10039

    authors: Mi J,Tian G,Liu S,Li X,Ni T,Zhang L,Wang B

    更新日期:2015-05-08 00:00:00

  • Control of source fertility on the eruptive activity of Piton de la Fournaise volcano, La Réunion.

    abstract::The eruptive activity of basaltic hotspot volcanoes displays major fluctuations on times scales of years to decades. Theses fluctuations are thought to reflect changes in the rate of mantle melt supply. However, the crustal filter generally masks the mantle processes involved. Here, we show that the cyclic and general...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-32809-0

    authors: Vlastélic I,Di Muro A,Bachèlery P,Gurioli L,Auclair D,Gannoun A

    更新日期:2018-09-27 00:00:00

  • The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803.

    abstract::Cyanobacteria exhibit a great capacity to adapt to different environmental conditions through changes in gene expression. Although this plasticity has been extensively studied in the model cyanobacterium Synechocystis sp. PCC 6803, a detailed analysis of the coordinated transcriptional adaption across varying conditio...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep22168

    authors: Hernández-Prieto MA,Semeniuk TA,Giner-Lamia J,Futschik ME

    更新日期:2016-02-29 00:00:00

  • Three cooperative mechanisms required for recovery after brain damage.

    abstract::Stroke is one of the main causes of human disabilities. Experimental observations indicate that several mechanisms are activated during the recovery of functional activity after a stroke. Here we unveil how the brain recovers by explaining the role played by three mechanisms: Plastic adaptation, hyperexcitability and ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-50946-y

    authors: Berger D,Varriale E,van Kessenich LM,Herrmann HJ,de Arcangelis L

    更新日期:2019-11-01 00:00:00

  • No influence of eye gaze on emotional face processing in the absence of conscious awareness.

    abstract::The human brain has evolved specialised mechanisms to enable the rapid detection of threat cues, including emotional face expressions (e.g., fear and anger). However, contextual cues - such as gaze direction - influence the ability to recognise emotional expressions. For instance, anger paired with direct gaze, and fe...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-52728-y

    authors: Caruana N,Inkley C,Zein ME,Seymour K

    更新日期:2019-11-07 00:00:00

  • Seq-SymRF: a random forest model predicts potential miRNA-disease associations based on information of sequences and clinical symptoms.

    abstract::Increasing evidence indicates that miRNAs play a vital role in biological processes and are closely related to various human diseases. Research on miRNA-disease associations is helpful not only for disease prevention, diagnosis and treatment, but also for new drug identification and lead compound discovery. A novel se...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-75005-9

    authors: Li J,Chen X,Huang Q,Wang Y,Xie Y,Dai Z,Zou X,Li Z

    更新日期:2020-10-21 00:00:00

  • Optical Characterization of Neurosurgical Operating Microscopes: Quantitative Fluorescence and Assessment of PpIX Photobleaching.

    abstract::Protoporphyrin IX (PpIX) induced by 5-aminolevulinic acid (5-ALA) is increasingly used as a fluorescent marker for fluorescence-guided resection of malignant gliomas. Understanding how the properties of the excitation light source and PpIX fluorescence interact with the surgical microscope is critical for effective us...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-30247-6

    authors: Belykh E,Miller EJ,Patel AA,Bozkurt B,Yağmurlu K,Robinson TR,Nakaji P,Spetzler RF,Lawton MT,Nelson LY,Seibel EJ,Preul MC

    更新日期:2018-08-22 00:00:00