Firalink: A bioinformatics pipeline for long non-coding RNA data analysis.
Journal
Non-coding RNA research
ISSN: 2468-0540
Titre abrégé: Noncoding RNA Res
Pays: Netherlands
ID NLM: 101688191
Informations de publication
Date de publication:
Dec 2023
Dec 2023
Historique:
received:
14
07
2023
revised:
08
09
2023
accepted:
08
09
2023
medline:
29
9
2023
pubmed:
29
9
2023
entrez:
29
9
2023
Statut:
epublish
Résumé
The Firalink bioinformatics pipeline has been developed to analyse long non-coding RNA (lncRNA) data generated by targeted sequencing. This pipeline has been first implemented for use with the FIMICS panel containing 2906 lncRNAs useful for investigations in cardiovascular disease. It has been subsequently tested and validated using a panel of lncRNAs targeting brain disease. The pipeline can be adapted to other targeted sequencing panels or other transcriptomics data (e.g. whole transcriptome) through a change of the reference genome/panel. Therefore, Firalink can be applied to different lncRNA panels and transcriptomics data targeting multiple diseases. The Firalink pipeline works on Linux and is freely available to non-commercial users at https://gitlab.lcsb.uni.lu/covirna/covirna-ext/covirna-firalink-pipeline. Access will be granted after contacting bioinformatics@firalis.com. The pipeline is implemented with the Nextflow workflow manager using Python and R scripts. It will remain available for at least two years following publication and will be regularly updated and upgraded. For an example of the application of the Firalink pipeline using the FIMICS panel, see www.covirna.eu.
Identifiants
pubmed: 37771472
doi: 10.1016/j.ncrna.2023.09.002
pii: S2468-0540(23)00058-6
pmc: PMC10523182
doi:
Types de publication
Journal Article
Langues
eng
Pagination
602-604Informations de copyright
© 2023 The Authors.
Déclaration de conflit d'intérêts
Y.D. owns patents related to diagnostic and therapeutic applications of RNAs. Y.D. and H.F. filed a patent on long noncoding RNAs for diagnostic, prognostic and therapeutic uses for pathologies and toxicities inducing heart disorders (WO2018229046). Firalis SA is commercializing the FIMICS and NeuroLINCs panels of long noncoding RNAs for heart and brain diseases.
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