• Designed specifically for bacterial ribosome sequencing
• Handles single-end sequencing reads

• Runs initial quality control checks on input reads
• Trims adapter sequences and low-quality bases
• Optionally handles UMI (Unique Molecular Identifier) sequences

• Aligns reads to ribosomal and transfer RNA sequences
• Aligns remaining reads to the reference genome
• Uses Bowtie for alignment with specified parameters
• Optionally removes duplicate reads

Counts gene expression using multiple methods:

• HTSeq-count for gene-level counts
• FeatureCounts for CDS and rRNA counts

Uses Plastid tools to generate detailed ribosome profiling data:

• Calculates ribosome positioning
• Creates count vectors
• Generates metagene profiles
• Analyzes ribosome footprint sizes and positions

• Handles different library strand types
• Allows custom adapter trimming
• Provides flexibility in read length and alignment parameters
• Can generate additional analyses for specific gene lists