RiboParser documentation

RiboParser is a modular command-line toolkit for comprehensive RNA-seq and Ribo-seq data analysis.

This documentation keeps the repository README short and moves the complete tutorial, parameter explanations, command templates, output interpretation, and helper scripts into a structured website.

Complete workflow

The first four steps belong to the public pipeline and can be handled by general bioinformatics tools (e.g. STAR, Bowtie, RSEM). The remaining steps are the RiboParser-specific analysis.

# 1-4: Public pipeline (general tools)
Reference preparation
→ Raw data download
→ Raw data cleaning
→ Alignment and quantification

# 5-10: RiboParser-specific analysis
→ Quality control
→ Gene-level analysis
→ Codon-level analysis
→ smORF analysis
→ SeRP analysis
→ Visualization and downstream analysis

Main command groups

Group	Commands
Ribo-quality	rpf_Reference, rpf_Check, rpf_Digest, rpf_Offset, rpf_Density, rpf_Merge, rpf_Periodicity, rpf_Metaplot, rpf_Coverage, rpf_Corr, rpf_Quant, rpf_Percent
RNA	rna_Offset, rna_Density
Ribo-pausing	rpf_Pausing, rpf_Occupancy, rpf_CoV, rpf_Cumulative_CoV, rpf_CDT, rpf_CST, rpf_Odd_Ratio, rpf_Meta_Codon
Ribo-utils	rpf_Shuffle, rpf_Shift, rpf_Retrieve, rpf_Bam2bw, rpf_Geneplot
smORF	smorf_scanner, smorf_cluster, smorf_evidence, smorf_quant
SeRP	serp_overlap, serp_peak, serp_properties

Helper scripts

Group	Commands	Purpose
Ribo-utils not covered above	rpf_Shuffle, rpf_Bam2bw, rpf_Retrieve	shuffled controls, signal track generation, retrieve rpf density
Ribo-utils merge helpers	merge_length, merge_saturation, merge_digestion, merge_offset, merge_offset_detail, merge_dst_list, merge_period, merge_metagene, merge_coverage, merge_quant, merge_pausing, merge_occupancy, merge_cdt, merge_cst, merge_odd_ratio	length distribution, gene saturation, rpf digestion, rpf offset, rpf offset details, rpf density file, 3nt periodicity, rpf metagene, rpf coverage, rpf quant, translation pausing score, translation occupancy, translation codon decoding time, translation codon selection time, translation codon odd ratio
FASTA helpers	fa_gc_sum, fa_len_flt, fa_len_sum, fa_split, line_feed, nt2aa, rand_seq, retrieve_seq, revs	sequence preprocessing and extraction
FASTQ helpers	fq_len_flt, fq_len_sum, fq_length, fq_split, fq_trim, fq2fa, fq2txt, phred_quality, simulate_fastq	read preprocessing and simulation
bedGraph helpers	bg2meta, rpm_smooth	signal processing
Bowtie/RSEM helpers	merge_bwt_log, merge_rsem	mapping and quantification summary
RiboCode/RiboTISH helpers	ribocode_bed_format, ribotish_format	external ORF-tool output formatting
Unix helpers	dos2unix	line-ending conversion
oligo helpers	get_overlap_seq, get_tissue_freq, get_win_seq	sequence-window and oligo-related processing