title: Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs.
abstract: The eukaryotic transcriptome is composed of thousands of coding and long non-coding RNAs (lncRNAs). However, we lack a software platform to identify both RNA classes in a given transcriptome. Here we introduce Annocript, a pipeline that combines the annotation of protein coding transcripts with the prediction of putative lncRNAs in whole transcriptomes. It downloads and indexes the needed databases, runs the analysis and produces human readable and standard outputs together with summary statistics of the whole analysis.
  
  
  METHODS
  Annocript is distributed under the GNU General Public License (version 3 or later) and is freely available at https://github.com/frankMusacchia/Annocript.
  
  
  BACKGROUND
  remo.sanges@szn.it.
authors.affiliation: Biology and Evolution of Marine Organisms, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy and Department of Biology, University of Naples Federico II, Via Mezzocannone 8, 80134, Naples, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Musacchia
authors.affiliation: Biology and Evolution of Marine Organisms, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy and Department of Biology, University of Naples Federico II, Via Mezzocannone 8, 80134, Naples, Italy.
authors.forename: Swaraj
authors.initials: S
authors.lastname: Basu
authors.affiliation: Biology and Evolution of Marine Organisms, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy and Department of Biology, University of Naples Federico II, Via Mezzocannone 8, 80134, Naples, Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Petrosino
authors.affiliation: Biology and Evolution of Marine Organisms, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy and Department of Biology, University of Naples Federico II, Via Mezzocannone 8, 80134, Naples, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Salvemini
authors.affiliation: Biology and Evolution of Marine Organisms, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy and Department of Biology, University of Naples Federico II, Via Mezzocannone 8, 80134, Naples, Italy.
authors.forename: Remo
authors.initials: R
authors.lastname: Sanges
mesh_terms: D006801:Humans; D058977:Molecular Sequence Annotation; D062085:RNA, Long Noncoding / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome
chemical_list: D062085:RNA, Long Noncoding