TY - JOUR
T1 - Firalink
T2 - A bioinformatics pipeline for long non-coding RNA data analysis
AU - Chauviere, Louis
AU - Hoffbeck, Lucien
AU - Shoaib, Muhammad
AU - Tessier, Florent
AU - Firat, Huseyin
AU - Satagopam, Venkata
AU - Devaux, Yvan
AU - COVIRNA consortium
N1 - Funding Information:
This work was supported by the EU Horizon 2020 project COVIRNA (grant agreement # 101016072). Y.D. has also received funding from the National Research Fund (grants #C14/BM/8225223 , C17/BM/11613033 and COVID-19/2020-1/14719577 /miRCOVID), the Ministry of Higher Education and Research , and the Heart Foundation-Daniel Wagner of Luxembourg .
Publisher Copyright:
© 2023 The Authors
PY - 2023/12
Y1 - 2023/12
N2 - 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. Availability and implementation: 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 [email protected]. 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. Supplementary information: For an example of the application of the Firalink pipeline using the FIMICS panel, see www.covirna.eu.
AB - 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. Availability and implementation: 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 [email protected]. 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. Supplementary information: For an example of the application of the Firalink pipeline using the FIMICS panel, see www.covirna.eu.
UR - http://www.scopus.com/inward/record.url?scp=85172028290&partnerID=8YFLogxK
UR - https://pubmed.ncbi.nlm.nih.gov/37771472
U2 - 10.1016/j.ncrna.2023.09.002
DO - 10.1016/j.ncrna.2023.09.002
M3 - Article
C2 - 37771472
AN - SCOPUS:85172028290
SN - 2468-0540
VL - 8
SP - 602
EP - 604
JO - Non-coding RNA Research
JF - Non-coding RNA Research
IS - 4
ER -