5 Other toolkits

This section intentionally avoids duplicating commands already documented in the workflow. It summarizes only auxiliary utilities and where to find them.

Utility groups

Group	Commands	Purpose
Ribo-utils not covered above	rpf_Shuffle, rpf_Shift, rpf_Bam2bw, rpf_Retrieve , rpf_Geneplot	shuffled controls, translation frame shift, signal track generation, retrieve rpf density, gene plotting
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