Availability – LncPipe is available at: https://github.com/likelet/LncPipe
LncPipe: A Nextflow-based pipeline for identification and analysis of long non-coding RNAs from RNA-Seq data
Recently, long noncoding RNA molecules (lncRNA) captured widespread attentions for its critical roles in diverse biological process and important implications in variety of human diseases and cancers. Identification and profiling of lncRNAs is a fundamental step to advance our knowledge on their function and regulatory mechanisms. However, RNA sequencing based lncRNA discovery is limited due to complicated operations and implementation. Researchers at Sun Yat-sen University Cancer Center have developed a one-stop pipeline called LncPipe focused on characterizing lncRNAs from raw transcriptome sequencing data. The pipeline was developed based on a popular workflow framework Nextflow, composed of four core procedures including reads alignment, assembly, identification and quantification. It contains various unique features such as well-designed lncRNAs annotation strategy, optimized calculating efficiency, diversified classification and interactive analysis report. Additionally, LncPipe allows users cancel pipeline, reset parameters from command or modifying main script directly and resume analysis from continues checkpoint.
Zhao Q, Sun Y, Wang D, Zhang H, Yu K, Zheng J, Zuo Z. (2018) LncPipe: A Nextflow-based pipeline for identification and analysis of long non-coding RNAs from RNA-Seq data. J Genet Genomics [Epub ahead of print]. [abstract]