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Protocols

Orione specifications

Information


Unique identifier OMICS_03698
Name Orione
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Gianmauro Cuccuru

Publication for Orione

Orione citations

 (18)
call_split

CD70 Deficiency due to a Novel Mutation in a Patient with Severe Chronic EBV Infection Presenting As a Periodic Fever

2018
Front Immunol
PMCID: 5796890
PMID: 29434583
DOI: 10.3389/fimmu.2017.02015
call_split See protocol

[…] his approach achieved an 86× average coverage over the 62Mb of target regions sequenced, with more than 95% regions covered. Data analysis has been performed using an analysis pipeline implemented in Orione (). Briefly, paired-end sequence reads were aligned to the human genome (hg19) with BWA-MEM [v.0.7.9a ()]. Initial mappings were processed using the GATK framework [version 2.8.1 ()], according […]

library_books

Comparative Genomics of Thalassobius Including the Description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov.

2018
Front Microbiol
PMCID: 5770400
PMID: 29375512
DOI: 10.3389/fmicb.2017.02645

[…] (Cuccuru et al., ). After filtering, the remaining reads were assembled using several software choices for comparative purposes: (i) Spades 3.0.0 (Bankevich et al., ) incorporated as a tool in Galaxy Orione Server, (ii) Seqman Ngen 12.0.1 (DNAstar), and (iii) Velvet 1.0.0 de novo assembler (Zerbino and Birney, ). After performance evaluation and comparison of metrics, the best assembly for each or […]

call_split

Draft Whole Genome Sequence of Psychrotrophic Arthrobacter sp. Strain 7749, Isolated from Antarctic Marine Sediments with Applications in Enantioselective Alcohol Oxidation

2017
Genome Announc
PMCID: 5658506
PMID: 29074668
DOI: 10.1128/genomeA.01197-17
call_split See protocol

[…] total of 1,005,914 single reads of 250 bp, representing 61× coverage of the strain 7749 genome. The trimmed reads were assembled de novo into 16 large contigs using SPAdes 3.0.0 () implemented on the Orione Galaxy server () (k-mer values of 21, 33, 55, 77, 99, and 127), giving 4,125,942 bp total length and an N50 contig size of 525,170 bp, with a largest contig of 779,368 bp. The contigs were scaf […]

library_books

Peeping into genomic architecture by re sequencing of Ochrobactrum intermedium M86 strain during laboratory adapted conditions

2016
Genom Data
PMCID: 4856823
PMID: 27222803
DOI: 10.1016/j.gdata.2016.04.003

[…] ther the quality of integrated contigs/scaffolds was evaluated using Check bacterial contigs tool . Whole pipeline of assembly was performed in NGS Galaxy Orione CRS4 . The contigs produced by Galaxy Orione CRS4 were merged into scaffolds using SSPACE tool . Contigs of O. intermedium M86 draft genome and resequenced genome were mapped against chromosome I and II of O. intermedium LMG 3301T and vis […]

library_books

Draft genome sequence and overview of the purple non sulfur bacterium Rhodopseudomonas palustris 42OL

2016
Stand Genomic Sci
PMCID: 4785650
PMID: 26966509
DOI: 10.1186/s40793-016-0145-y

[…] Genes were identified using the prokaryotic genome annotation software Prokka 1.4.0 [] (Galaxy Orione server []). For gene finding and translation, Prokka makes use of the program Prodigal []. Homology searching (BLAST, hmmscan) was then performed using the translated protein sequences as queri […]

library_books

Draft genome of Leisingera aquaemixtae CECT 8399T, a member of the Roseobacter clade isolated from a junction of fresh and ocean water in Jeju Island, South South Korea

2016
Genom Data
PMCID: 4778666
PMID: 26981415
DOI: 10.1016/j.gdata.2016.01.010

[…] also included in Galaxy Orione Web Server. The 40 contigs had a N50 of 339,773 bp and summarize 4,614,060 bp with a G + C content of 64.4%.This draft genome was annotated with Prokka , within Galaxy Orione Server, and RAST v.2.0 using default parameters. Further analysis of annotated genome by Prokka was done with different web servers. WebMGA Server was used to search for COGs, NCBI Batch CD-S […]

Citations

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Orione institution(s)
CRS4, Science and Technology Park Polaris, Piscina Manna, Pula (CA), Italy
Orione funding source(s)
Supported by the Sardinian Regional Authorities and the Wellcome Trust (095931).

Orione review

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Anonymous user #724

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Web
Fantastic ! Great Tool