FRAMA specifications


Unique identifier OMICS_11024
Alternative name from RNA-seq to annotated mRNA assembly
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A reference transcriptome and RNA-seq data.
Input format GenBank, FASTQ
Output data A representative compilation of transcripts, a so-called transcript catalog, with CDSs and mRNA boundaries annotated.
Operating system Unix/Linux
Programming languages Perl, R
Computer skills Advanced
Version 20151019
Stability Stable
Requirements Trinity, samtools, bamtools, bowtie/bowtie2, EMBOSS, MAFFT, GENSCAN, RepeatMasker, CD-HIT-EST, TGICL, WU-BLAST, NCBI-BLAST, GenblastA, Perl::BioPerl, Parallel::ForkManager, Set::IntSpan, FileHandle::Unget, R::plyr, ggplot, reshape, gridExtra, annotate, GO.db, KEGG.db
Maintained Yes



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  • person_outline Martin Bens <>
  • person_outline Karol Szafranski <>

Publication for from RNA-seq to annotated mRNA assembly

FRAMA institution(s)
Leibniz Institute on Ageing - Fritz Lipmann Institute, Jena, Germany; Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
FRAMA funding source(s)
Supported by the Bundesministerium für Bildung und Forschung (BMBF) and the Leibniz-Gesellschaft through the Senatsausschusswettbewerb (SAW), grant SAW-2012-FLI-2, as well as the Deutsche Forschungsgemeinschaft (DFG), grant PL 173/8-1.

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