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Rnnotator specifications


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


No version available

Publication for Rnnotator

Rnnotator citations


Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi

Sci Rep
PMCID: 5910433
PMID: 29679020
DOI: 10.1038/s41598-018-24686-4

[…] e single mitochondrial contigs for each genome. Illumina reads of stranded RNA-seq data were used as the input for de novo assembly of RNA contigs. Reads were assembled into consensus sequences using Rnnotator (v. 3.3.2).Both genomes were annotated using the JGI Annotation Pipeline and made available via the JGI fungal portal MycoCosm. The genomes of Cadophora sp. and P. macropsinosa can be access […]


Genome Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors

Front Microbiol
PMCID: 5840194
PMID: 29551995
DOI: 10.3389/fmicb.2018.00276
call_split See protocol

[…] nce genome, Illumina genomic reads from two libraries were filtered and assembled with AllPathsLG (Gnerre et al., ). RNA-seq data for each genome were de novo assembled into consensus sequences using Rnnotator (Martin et al., ). The genome assembly was annotated using the JGI Annotation Pipeline and made available via the JGI fungal genome portal MycoCosm (jgi.doe.gov/fungi; Grigoriev et al., ). T […]


Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus

PMCID: 5473757
PMID: 28450370
DOI: 10.1534/g3.117.039396

[…] then assembled together with the original Illumina library with AllPathsLG (). RNA-seq data were used as input for de novo assembly of RNA contigs. Reads were assembled into consensus sequences using Rnnotator (). Both inputs were used to annotate genomes with the DOE-JGI Annotation pipeline, and release data in the DOE-JGI fungal genome portal MycoCosm (http://jgi.doe.gov/fungi; ).Illumina librar […]


Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Genome Biol
PMCID: 5307856
PMID: 28196534
DOI: 10.1186/s13059-017-1151-0

[…] as used to determine the concentration of the libraries. Libraries were sequenced on the Illumina Hiseq in 2 × 100 bp read format. Illumina reads were de novo assembled into consensus sequences using Rnnotator (v. 2.5.2 or later) []. For A. aculeatus, cDNA libraries were generated using the cDNA Rapid Library Preparation Kit (Roche). mRNA was purified from total RNA using Absolutely mRNA™ purifica […]


Draft Genome Sequence of the White Rot Fungus Obba rivulosa 3A 2

Genome Announc
PMCID: 5026439
PMID: 27634999
DOI: 10.1128/genomeA.00976-16

[…] h 3-kbp insert, which was then assembled with the original Illumina library with AllPaths-LG release 46652 () to produce the 34.04-Mbp assembly in 712 scaffolds. The transcriptome was assembled using Rnnotator (). The genome was annotated using the JGI annotation pipeline, resulting in 13,206 predicted genes.The assembly length and estimated number of genes are typical of saprobic basidiomycetes. […]


Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum

Nat Commun
PMCID: 5023957
PMID: 27601008
DOI: 10.1038/ncomms12662

[…] stellatum, library construction and 2 × 100 bp Illumina HiSeq sequencing was performed by Beckman Coulter Genomics (Danvers, MA, USA) using their standard protocols.RNA-Seq reads were assembled using Rnnotator v.2.5.6 or later or CLC Genomics Workbench v6 or later (Qiagen) after trimming and filtering for low-quality, low-complexity, adaptor and duplications. Assembled contigs of at least 100 bp l […]


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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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