FRAMA specifications

Unique identifier:
OMICS_11024
Software type:
Pipeline/Workflow
Restrictions to use:
Academic or non-commercial use
Input format:
GenBank, FASTQ
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Name:
from RNA-seq to annotated mRNA assembly
Interface:
Command line interface
Input data:
A reference transcriptome and RNA-seq data.
Output data:
A representative compilation of transcripts, a so-called transcript catalog, with CDSs and mRNA boundaries annotated.
Programming languages:
Perl, R
Version:
20151019
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

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FRAMA distribution

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FRAMA support

Documentation

Maintainers

  • Martin Bens <>
  • Karol Szafranski <>

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Publications

Institution(s)

Leibniz Institute on Ageing - Fritz Lipmann Institute, Jena, Germany; Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany

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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