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Rnnotator | An automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

Assembles Illumina single or paired-end reads and incorporates strand-specific RNA-Seq reads into the assembly. Rnnotator is an automated software pipeline that consists of three major components: preprocessing of reads, assembly, and post-processing of contigs. In the absence of a reference transcriptome, the software can produce a set of transcripts directly from RNA-Seq reads. It was applied to two yeast transcriptomes and the results were compared to the reference gene catalogs of these organisms.

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Rnnotator classification

Rnnotator specifications

Unique identifier:
Command line interface
Input data:
Short read sequences.
Biological technology:
Computer skills:
Software type:
Package/Module, Pipeline/Workflow
Restrictions to use:
Academic or non-commercial use
Output data:
Assembled transcript contigs.
Operating system:

Rnnotator distribution


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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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