Rnnotator protocols

Rnnotator specifications

Information


Unique identifier OMICS_01323
Name Rnnotator
Software type Package/Module, Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Short read sequences.
Output data Assembled transcript contigs.
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

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Publication for Rnnotator

Rnnotator IN pipelines

 (4)
2013
PMCID: 3765226
PMID: 23957668
DOI: 10.1186/1471-2164-14-563

[…] (pacific biosciences) sequencing of a. tequilana cdnas [32] (methods) (figure 2a). error-corrected, high quality subreads (n50 = 450 bp, additional file 1: figure s2) (methods) were aligned to the rnnotator de novo assembly (figure 2a). we observed that 4,766 of 4,767 subreads are represented in the short-read based de novo agave transcriptome assembly. we also compared the a. tequilana […]

2013
PMCID: 3765226
PMID: 23957668
DOI: 10.1186/1471-2164-14-563

[…] the rnnotator de novo assembly (figure 2a). we observed that 4,766 of 4,767 subreads are represented in the short-read based de novo agave transcriptome assembly. we also compared the a. tequilana rnnotator assembly to all 82 a. tequilana nucleotide sequences available from genbank and observed that 81 (98.8%) are represented in our dataset (figure 2a). comparison of our a. tequilana rnnotator […]

2013
PMCID: 3765226
PMID: 23957668
DOI: 10.1186/1471-2164-14-563

[…] rnnotator assembly to all 82 a. tequilana nucleotide sequences available from genbank and observed that 81 (98.8%) are represented in our dataset (figure 2a). comparison of our a. tequilana rnnotator assembly to a set of 12,972 transcripts assembled from low-depth rna sequencing by mckain et al.[27] (approximately 3 gbp, compared to 293 gbp in the present study) (figure 2a) reveals […]

2013
PMCID: 3765226
PMID: 23957668
DOI: 10.1186/1471-2164-14-563

[…] transcriptome assembly and 8,298 transcript contigs (64.0%) align with no insertions or deletions. of transcript contigs aligning between the two de novo assemblies, 6,578 (50.7%) are longer in the rnnotator de novo assembly. taken together, these comparisons further support the accuracy and near-completeness of our reference transcriptome dataset., the transcriptomes of a. deserti and a. […]

Rnnotator institution(s)
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA; School of Public Health, LSU-Health Sciences Center, New Orleans, LA, USA; Department of Genetics, Stanford University Medical School, Stanford, CA, USA

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