REGIS v1.0.5 is a comprehensive lncRNA identification pipeline implemented in Go with a modern Terminal User Interface (TUI). It performs:

• Quality control with FastQC
• Adapter trimming with Trimmomatic
• rRNA filtering with SortMeRNA (NEW in v1.0.5)
• De novo assembly with Trinity OR reference-based alignment with HISAT2
• Transcript assembly with StringTie
• Multi-tool coding potential assessment (CPC2 + CPAT for high-confidence predictions)
• Expression quantification with featureCounts
• Novel lncRNA classification with gffcompare
• Secondary structure prediction with RNAfold
• lncRNA-mRNA interaction prediction with LncTar
• RNA-RNA interaction cross-validation with IntaRNA
• Consensus target analysis
• Gene list building for enrichment analysis (getENRICH-ready)
• Comprehensive visualization (IGV reports, RSeQC, MultiQC)

NEW in v1.0.1: - Go implementation with TUI (Terminal User Interface) - SortMeRNA integration for rRNA filtering - Automatic SILVA database download - Background gene list generation for enrichment - Real-time progress tracking with animated TUI - System resource monitoring (CPU/Memory) - Interactive help and command display

The pipeline supports both single-end and paired-end data, and can work with or without a reference genome.

REGIS Team: Dr. Jitendra Narayan (Principal Investigator) Dr. Stefano Tiozzo (CNRS-Sorbonne University) Pranjal Pruthi (Researcher Programmer, CSIR IGIB)

Funded by The Rockefeller Foundation and CSIR-IGIB.