Orione, a web-based framework for NGS analysis in microbiology

scientific article (publication date: July 2014)

Orione, a web-based framework for NGS analysis in microbiology is …
instance of (P31):
scholarly articleQ13442814

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P8978DBLP publication IDjournals/bioinformatics/CuccuruOPSSTUZF14
P356DOI10.1093/BIOINFORMATICS/BTU135
P3181OpenCitations bibliographic resource ID2211838
P932PMC publication ID4071203
P698PubMed publication ID24618473
P5875ResearchGate publication ID260717409

P50authorPaolo UvaQ50728670
Nicola SoranzoQ56486995
Gianluigi ZanettiQ57544848
Nicole SoranzoQ28050073
Massimiliano OrsiniQ29048220
P2093author name stringGianmauro Cuccuru
Andrea Pinna
Antonella Travaglione
Giorgio Fotia
Andrea Sbardellati
P2860cites workMetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence readsQ36368703
De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computerQ36586588
EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes.Q36702597
High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity.Q38032123
Assembling millions of short DNA sequences using SSAKE.Q51926970
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciencesQ21092859
BFAST: an alignment tool for large scale genome resequencingQ21142709
Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeQ21183894
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequenceQ24544402
Metagenomic microbial community profiling using unique clade-specific marker genesQ24599864
Ab initio gene identification in metagenomic sequencesQ24620886
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencingQ24629733
Identifying bacterial genes and endosymbiont DNA with GlimmerQ24653724
Fast and accurate short read alignment with Burrows-Wheeler transformQ24653853
Velvet: algorithms for de novo short read assembly using de Bruijn graphsQ24657623
BLAT—The BLAST-Like Alignment ToolQ24682492
Fast gapped-read alignment with Bowtie 2Q27860699
OMERO: flexible, model-driven data management for experimental biologyQ28260901
SOAP: short oligonucleotide alignment programQ28266228
SHRiMP2: sensitive yet practical SHort Read MappingQ28304260
ABySS: a parallel assembler for short read sequence dataQ29547263
Scaffolding pre-assembled contigs using SSPACEQ29616857
SOPRA: Scaffolding algorithm for paired reads via statistical optimizationQ33615353
Interactive metagenomic visualization in a Web browserQ34036161
Lentiviral hematopoietic stem cell gene therapy benefits metachromatic leukodystrophyQ34356914
SEQuel: improving the accuracy of genome assembliesQ36022139
P275copyright licenseCreative Commons Attribution-NonCommercial 3.0 UnportedQ18810331
P6216copyright statuscopyrightedQ50423863
P433issue13
P407language of work or nameEnglishQ1860
P921main subjectcomputational mathematicsQ1122491
P1104number of pages2
P304page(s)1928-1929
P577publication date2014-03-10
P1433published inBioinformaticsQ4914910
P1476titleOrione, a web-based framework for NGS analysis in microbiology
P478volume30

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cites work (P2860)
Q47864536A New COL3A1 Mutation in Ehlers-Danlos Syndrome Vascular Type With Different Phenotypes in the Same Family.
Q92323986BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology
Q46244262Bacterial Succession on Sinking Particles in the Ocean's Interior
Q28115028Bi-allelic Mutations in KLHL7 Cause a Crisponi/CISS1-like Phenotype Associated with Early-Onset Retinitis Pigmentosa
Q34234832BioBlend.objects: metacomputing with Galaxy
Q53226516Buried in the Middle but Guilty: Intronic Mutations in the TCIRG1 Gene Cause Human Autosomal Recessive Osteopetrosis.
Q50043168CD70 Deficiency due to a Novel Mutation in a Patient with Severe Chronic EBV Infection Presenting As a Periodic Fever.
Q118110051Collinsella urealyticum sp. nov., a urease-positive bacterial strain isolated from swine faeces
Q35757232Comparative Genomics and Characterization of Hybrid Shigatoxigenic and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains
Q48503145Comparative Genomics of Thalassobius Including the Description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov.
Q39671870Comparative genomic analysis of seven Mycoplasma hyosynoviae strains
Q37731100Complete Genome Sequences of Two Escherichia coli Phages, vB_EcoM_ ESCO5 and vB_EcoM_ESCO13, Which Are Related to phAPEC8.
Q45200810Complete genome sequence of mitochondrial DNA (mtDNA) of Chlorella sorokiniana
Q47952153Complete sequence and characterization of mitochondrial and chloroplast genome of Chlorella variabilis NC64A.
Q47873530Complete sequence of human mitochondrial DNA obtained by combining multiple displacement amplification and next-generation sequencing on a single oocyte
Q46251992Computational profiling of the gut-brain axis: microflora dysbiosis insights to neurological disorders
Q36381842Draft Genome Sequence of CO33, a Coffee-Infecting Isolate of Xylella fastidiosa.
Q41768388Draft Genome Sequence of Pseudomonas putida JLR11, a Facultative Anaerobic 2,4,6-Trinitrotoluene Biotransforming Bacterium
Q35098825Draft Genome Sequence of the Xylella fastidiosa CoDiRO Strain
Q35977717Draft Genome Sequences of 19 Salmonella enterica Serovar Typhimurium [4,5:i:-] Strains Resistant to Nalidixic Acid from a Long-Term Outbreak in Italy.
Q30917416Draft Genome Sequences of Sanguibacteroides justesenii, gen. nov., sp. nov., Strains OUH 308042T (= ATCC BAA-2681T) and OUH 334697 (= ATCC BAA-2682), Isolated from Blood Cultures from Two Different Patients
Q42620193Draft Whole-Genome Sequence of Psychrotrophic Arthrobacter sp. Strain 7749, Isolated from Antarctic Marine Sediments with Applications in Enantioselective Alcohol Oxidation
Q38783955Draft genome of Leisingera aquaemixtae CECT 8399(T), a member of the Roseobacter clade isolated from a junction of fresh and ocean water in Jeju Island, South Korea
Q36629177Draft genomic sequence of Nereida ignava CECT 5292(T), a marine bacterium of the family Rhodobacteraceae
Q37378708Epithelial Coculture and l-Lactate Promote Growth of Helicobacter cinaedi under H2-Free Aerobic Conditions
Q40372761Genome Sequences of Seven Mycoplasma hyosynoviae Strains Isolated from the Joint Tissue of Infected Swine (Sus scrofa).
Q46090917High Throughput Sequencing for Detection of Foodborne Pathogens.
Q35589786Influence of a non-hospital medical care facility on antimicrobial resistance in wastewater
Q30946725IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data.
Q35763834NCBI BLAST+ integrated into Galaxy.
Q37383539Next-generation sequencing and a novel COL3A1 mutation associated with vascular Ehlers-Danlos syndrome with severe intestinal involvement: a case report
Q56999089Next-generation sequencing revolution through big data analytics
Q61448622Novel ANKRD11 gene mutation in an individual with a mild phenotype of KBG syndrome associated to a GEFS+ phenotypic spectrum: a case report
Q36870098Peeping into genomic architecture by re-sequencing of Ochrobactrum intermedium M86 strain during laboratory adapted conditions
Q28606500Publishing and sharing multi-dimensional image data with OMERO
Q42797186Rare Detection of the Acinetobacter Class D Carbapenemase blaOXA-23 Gene in Proteus mirabilis
Q36254978SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology
Q36215010Serological and Virological Evidence of Crimean-Congo Haemorrhagic Fever Virus Circulation in the Human Population of Borno State, Northeastern Nigeria.
Q37535764Whole-Genome Characterization and Strain Comparison of VT2f-Producing Escherichia coli Causing Hemolytic Uremic Syndrome.
Q93131511Whole-Genome Sequence of Listeria monocytogenes Serovar 1/2a Strain IZSAM_Lm_15_17439_A144, Representative of a Human Outbreak in 2008
Q35173226Whole-Genome Sequence of Listeria monocytogenes Serovar 4b Strain IZSAM_Lm_hs2008, Isolated from a Human Infection in Italy
Q60045066Whole-Genome Sequence of a Reemerging Listeria monocytogenes Serovar 1/2a Strain in Central Italy
Q92795392Whole-Genome Sequencing of Multidrug-Resistant Escherichia coli Strains Harboring the mcr-1 Gene, Isolated from Seawater of the Algiers Coast in Algeria
Q42211026Whole-Genome Sequencing of Mycoplasma mycoides subsp. mycoides Italian Strain 57/13, the Causative Agent of Contagious Bovine Pleuropneumonia.
Q92992977Whole-Genome Sequencing of Six Strains of Salmonella enterica Isolated from Imported Meat in Algeria
Q92463011Whole-genome sequencing of Listeria monocytogenes serotype 4b isolated from ready-to-eat lentil salad in Algiers, Algeria
Q55385702Xapuri virus, a novel mammarenavirus: natural reassortment and increased diversity between New World viruses.
Q42975797iReport: a generalised Galaxy solution for integrated experimental reporting.

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