Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs

Bioinformatics
Francesco MusacchiaRemo Sanges

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. Annocript is distributed under the GNU General Public License (version 3 or later) and is freely available at https://github.com/frankMusacchia/Annocript. remo.sanges@szn.it.

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Citations

Jun 20, 2015·Frontiers in Bioengineering and Biotechnology·Dario VenezianoAlfredo Ferro
May 18, 2016·Marine Genomics·Rute R da FonsecaRicardo J Pereira
Jun 14, 2016·Omics : a Journal of Integrative Biology·Natalia de Souza AraujoMaria Cristina Arias
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Mar 6, 2018·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Eugenia SanchezSebastian Steinfartz
Apr 29, 2018·BMC Genomics·Priscila Karla F SantosMaria Cristina Arias
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Jan 17, 2020·GigaScience·Rute R da FonsecaM Thomas P Gilbert
Mar 25, 2017·BMC Bioinformatics·Giovanna M M VentolaLuigi Cerulo
Oct 13, 2017·BMC Genomics·Fabrizio LombardoBruno Arcà
Mar 23, 2018·AoB Plants·Sumetha KannanElizabeth R Waters
Jan 25, 2020·Scientific Reports·Danilo Guillermo CeschinAndrés Venturino
Jul 11, 2018·Journal of Neurovirology·Xiang GuanZheng-Fei Liu
Jun 10, 2020·Proceedings of the National Academy of Sciences of the United States of America·Yukiteru NakayamaIchiro Manabe
Apr 1, 2020·Frontiers in Plant Science·Hikmet BudakHalise Busra Cagirici
Feb 20, 2019·Functional & Integrative Genomics·Aleksandra LipkaBozena Szafranska
May 29, 2018·International Journal of Genomics·Qing ChenYan Wang
Dec 18, 2020·Briefings in Bioinformatics·A T Vivek, Shailesh Kumar
Feb 27, 2021·Scientific Reports·Fatemeh SalabiAyeh Sadat Sadr

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