Orione protocols

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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 in pipelines

 (5)
2018
PMCID: 5796890
PMID: 29434583
DOI: 10.3389/fimmu.2017.02015

[…] 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 ()], […]

2016
PMCID: 4770636
PMID: 26929790
DOI: 10.1186/s40793-016-0141-2

[…] 1,000 nucleotides and had a total size of 2,888,349 bp. an average 77x coverage depth was accomplished., the draft genome was annotated using prokka [], an open source software tool, within galaxy orione server, and using rast v2.0 (rapid annotation using subsystem technology) []. crispr repeats were examined by crispr finder []. signal peptides were searched using signal p 4.1 server []. […]

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

[…] with 205,596,181 bp, which resulted in a sequencing coverage of 45 ×., reads were analyzed for quality control with the program fastqc, developed by babraham bioinformatics, and wrapped in galaxy orione server . after filtering and trimming, the remaining reads were assembled using spades 3.0.0 and mira . spades scaffolds bigger than 1000 pb and with coverage larger than 10 × were selected […]

2015
PMCID: 4384128
PMID: 25814588
DOI: 10.1128/genomeA.00005-15

[…] of 328 and 596 meganucleotides for ouh 308042t and ouh 334696, respectively., the reads were assembled de novo using the spades 3.0.0 assembler implemented on the orione galaxy web server (http://orione.crs4.it/), with k values equal to 21, 33, 55, 77, 99, and 127, as suggested in the spades 3.0.0 manual, and contigs of <500 bp in length were removed (, ). following submission to the ncbi […]

2015
PMCID: 4384145
PMID: 25814605
DOI: 10.1128/genomeA.00197-15

[…] platform, obtaining 427,523 single-end reads spanning from 20 to 400 nucleotides. the quality-filtered reads were assembled into contigs and annotated using a dedicated workflow available at the orione website (), which uses spades () and prokka, respectively (). finishing and annotation were manually curated., the m. mycoides subsp. mycoides strain 57/13 genome contains […]


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Orione in publications

 (20)
PMCID: 5796890
PMID: 29434583
DOI: 10.3389/fimmu.2017.02015

[…] 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 ()], […]

PMCID: 5773550
PMID: 29348516
DOI: 10.1038/s41598-018-19446-3

[…] mila_002_bis, mila_003, mila_004, mila_004_dir, mila_005, mila_006, mila_006_dir, mila_007_dir, mila_008_dir, mila_009_dir, nanda_001, nettuno_001, nuccia_001, olga_001, onda_001, oreste_001, orione_est_001, orlando_001, orlando_002, oscar_ovest_001, pachino_004, palma_001, palma_002, palma_003, pamela_001, pamela_001_bis, pancrazio_sud_001, paola_est_001, patty_est_001, […]

PMCID: 5770400
PMID: 29375512
DOI: 10.3389/fmicb.2017.02645

[…] reads. the illumina reads were analyzed for quality control using fastqc, a common quality control tool developed by babraham bioinformatics to check raw sequencing data, which is wrapped in galaxy orione server (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 […]

PMCID: 5658506
PMID: 29074668
DOI: 10.1128/genomeA.01197-17

[…] 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 […]

PMCID: 5306315
PMID: 28261134
DOI: 10.3389/fpsyg.2017.00200

[…] la volpe e l'orso” (“the fisherman, the fox, and the bear,” 15 questions, e.g., “which of these sentences is more important for the development of the plot?” 503 words);, eighth grade, “don orione” (“father orione,” 15 questions, e.g., “which word would you choose to substitute the term “herd”?” 193 words);, ninth grade, “piaggia” (“piaggia,” 15 questions, e.g., “why was the rifle […]


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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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Fantastic ! Great Tool