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Protocols

Oases specifications

Information


Unique identifier OMICS_01322
Name Oases
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Roche
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 0.2.09
Stability Stable
Maintained Yes

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Versioning


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Documentation


Maintainers


  • person_outline Marcel Schulz
  • person_outline Daniel Zerbino

Publication for Oases

Oases citations

 (255)
library_books

The aquatic animals’ transcriptome resource for comparative functional analysis

2018
BMC Genomics
PMCID: 5954267
PMID: 29764375
DOI: 10.1186/s12864-018-4463-x

[…] To ensure more complete assembly, we used three de novo assembly tools: Oases (v0.2.08, requiring Velvet v1.2.09) [, ], SOAPdenovo-Trans (release 1.02) [], and Trinity (release 2013–02-25) [] that based on the de Bruijn graphs. Previous reports suggest that coverage in tr […]

library_books

Transcriptome profiling of the honeybee parasite Varroa destructor provides new biological insights into the mite adult life cycle

2018
BMC Genomics
PMCID: 5936029
PMID: 29728057
DOI: 10.1186/s12864-018-4668-z

[…] The read quality of the RNA-seq libraries was evaluated using FastQC []. Cleaned and filtered reads were de novo assembled using DRAP version 1.7 (de novo RNA-seq Assembly Pipeline) [] with the Oases assembler [] and filtered with at least one FPKM. The resulting contigs were aligned with NCBI blast (blastx program, version 2.2.26, e-value under 1e-5) on Refseq protein, Swissprot and Ensembl […]

call_split

A Possible Trifunctional β Carotene Synthase Gene Identified in the Draft Genome of Aurantiochytrium sp. Strain KH105

2018
Genes
PMCID: 5924542
PMID: 29642531
DOI: 10.3390/genes9040200
call_split See protocol

[…] equences, 150 bp ×2). A total of 113.6 Gbp nucleotide (Gbn) sequence data were obtained, 71.8% of which (81.6 Gbn) had a quality value ≥30. These high-quality sequences were assembled with the Velvet/Oases assembler with a hash length of 37 []. Trinity assemblies were also used []. As a result, we obtained 112,852 contigs (29.3 Mbp) over 100 bp with an N50 size of 1575 bp. Of these, 88,570 (78%) h […]

library_books

Sequence analysis of the potato aphid Macrosiphum euphorbiae transcriptome identified two new viruses

2018
PLoS One
PMCID: 5875755
PMID: 29596449
DOI: 10.1371/journal.pone.0193239

[…] iversity of gene expression patterns and consequently a more comprehensive transcriptome set to be derived. The reads were de novo assembled into 22,137 contigs (N50 = 2,130 bp) using the SEED/Velvet/Oases approach []. Various de novo transcriptome assembly algorithms are freely available. Each has advantages and disadvantages and one has to choose among different assemblers the most suitable for […]

library_books

Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome based markers

2018
BMC Genet
PMCID: 5872505
PMID: 29587653
DOI: 10.1186/s12863-018-0603-1

[…] r. 1.0.3 and Trinity ver. 2.1.1 [] in sequencing reads derived from control condition. Contigs assembled by Velvet-Oases used various kmer-sizes (39, 49, 59, 69, 79, 89 and 99)(Velvet version 1.2.10, Oases version 0.2.8), and all the contigs assembled by various kmer-sizes were merged into a contig. Contigs assembled by either SOAPdenovo-Trans or Trinity used optimized K-mers. There are three asse […]

library_books

A global ocean atlas of eukaryotic genes

2018
Nat Commun
PMCID: 5785536
PMID: 29371626
DOI: 10.1038/s41467-017-02342-1

[…] al RNA-like reads were excluded using sortmeRNA. Resulting reads from each metatranscriptomic sample were assembled using velvet v.1.2.07 with a kmer size of 63. Isoform detection was performed using oases 0.2.08. Contigs smaller than 150 bp were removed from further analysis. Assembly results and descriptive statistics for each sample are shown in Supplementary Data . Similar sequences from more […]


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Oases institution(s)
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany

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