Oases 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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Maintainers


  • person_outline Marcel Schulz <>
  • person_outline Daniel Zerbino <>

Publication for Oases

Oases IN pipelines

 (8)
2017
PMCID: 5386861
PMID: 28159865
DOI: 10.1534/g3.117.040089

[…] (1) the clc bio algorithm based on de bruijn graphs and the optimized parameters, defined as word size = 64, bubble size = 500, length fraction = 0.98, and similarity fraction = 0.98; and (2) oases v0.2.08 with k-mer sizes of 53, 59, 65, 71, 77, 83, and 89 (schulz et al. 2012). to obtain the set of nonredundant transcripts for each assembly, transcripts with ≥90% sequence similarity […]

2016
PMCID: 5078956
PMID: 27776492
DOI: 10.1186/s12864-016-3119-y

[…] and reproductive output in the silent treatment., to assess the gene expression profiles, sequenced reads from all 24 individuals were mapped to a de novo transcriptome, which we assembled with oases (see methods). we used rsem version 1.2.0 with default settings [43] to assign reads to isoforms and to calculate transcript abundance. from all 24 samples, an average of 97 % of reads […]

2015
PMCID: 4391584
PMID: 25880642
DOI: 10.1186/s12864-015-1460-1

[…] retained (figure 1, table 1) and filtered for quality, resulting in 185,410,176 high quality illumina sequences that were used in a de novo transcriptome assembly using the transcriptome assembler oases [38]. a total of 159,755,431 (86.16%) reads were assembled into 165,668 transcripts including isoforms (table 2). possible contaminants in the transcript assemblies were identified and removed […]

2014
PMCID: 3962355
PMID: 24658574
DOI: 10.1371/journal.pone.0091101

[…] mapped to the s. microadriaticum transcriptome, and a significant reduction in potential chimeric locus assemblies for the remaining 16,555,086 read pairs., the transcriptome was assembled with oases [48] using k-mer values ranging from 29 to 69. to reduce redundancy within single k-mer assemblies, only contigs with a minimum coverage of 7 were reported. based on contig lengths, number […]

2014
PMCID: 3969326
PMID: 24682075
DOI: 10.1371/journal.pone.0092087

[…] using two software tools based on the de bruijn graph algorithm. we used velvet (v1.2.07) [20] to assess k-mer sizes and assemble contigs. we joined the contigs into transcript isoforms using oases (v0.2.08), which was specially developed for the de novo assembly of transcripts using short reads [21]. we considered several hash lengths to select the best de novo assembly. a schematic […]

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

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