Riboseq Metro
Ribosome profiling with matched RNA-seq and TI-seq, covering multi-tool ORF calling, P-site identification, and translational efficiency analysis with cross-sample ORF merging.
Mermaid source
%%metro title: nf-core/riboseq%%metro logo: nf-core-riboseq_logo_light.png | nf-core-riboseq_logo_dark.png%%metro logo_scale: 1.15%%metro center_ports: true%%metro style: nfcore%%metro diamond_style: symmetric%%metro directional: true%%metro file: fastq_in | FASTQ%%metro file: hybrid_gtf_out | GTF | Hybrid GTF%%metro file: orf_catalogue | BED | ORF catalogue%%metro file: bigwig_out | BW | Coverage%%metro file: counts_out | TSV | Gene counts%%metro file: psite_orf_out | TSV | ORF P-site counts%%metro file: psite_gene_out | TSV | Gene P-site counts%%metro file: te_out | TSV | TE results%%metro file: report_final | HTML | MultiQC%%metro line: riboseq | Ribo-seq | #e6007e%%metro line: rnaseq | Matched RNA-seq | #2db572%%metro line: tiseq | TI-seq | #2b6cb0%%metro line: annotation | Hybrid annotation | #f2b407
%%metro grid: preprocessing, alignment, novel_transcripts | 0,0%%metro grid: orf_calling, psite_id, te, reporting | 0,1%%metro x_spacing: 70%%metro legend: br | 10,130
graph LR subgraph preprocessing [Read pre-processing] fastq_in[ ] umi_extract[UMI-tools extract] fastp[fastp] trimgalore[Trim Galore!] bbsplit[BBSplit] sortmerna[SortMeRNA] ribodetector[RiboDetector] bowtie2_rrna[Bowtie2] fastqc[FastQC] infer_strand[Infer strandedness] equalise[Equalise\nread lengths]
fastq_in -->|riboseq,rnaseq,tiseq| umi_extract umi_extract -->|riboseq,rnaseq,tiseq| fastp umi_extract -->|riboseq,rnaseq,tiseq| trimgalore fastp -->|riboseq,rnaseq,tiseq| bbsplit trimgalore -->|riboseq,rnaseq,tiseq| bbsplit bbsplit -->|riboseq,rnaseq,tiseq| sortmerna bbsplit -->|riboseq,rnaseq,tiseq| ribodetector bbsplit -->|riboseq,rnaseq,tiseq| bowtie2_rrna sortmerna -->|riboseq,rnaseq,tiseq| fastqc ribodetector -->|riboseq,rnaseq,tiseq| fastqc bowtie2_rrna -->|riboseq,rnaseq,tiseq| fastqc fastqc -->|riboseq,rnaseq,tiseq| infer_strand infer_strand -->|riboseq,rnaseq,tiseq| equalise end
subgraph alignment [Alignment & quantification] star[STAR] umi_dedup[UMI-tools dedup] genomecov[BEDTools\ngenomecov] salmon_quant[Salmon] bigwig_out[ ] counts_out[ ]
star -->|riboseq,rnaseq,tiseq| umi_dedup umi_dedup -->|riboseq,rnaseq,tiseq| genomecov genomecov -->|riboseq,rnaseq,tiseq| bigwig_out umi_dedup -->|riboseq,rnaseq,tiseq| salmon_quant salmon_quant -->|riboseq,rnaseq,tiseq| counts_out end
subgraph novel_transcripts [Transcript discovery] stringtie[StringTie] gffcompare[gffcompare] hybrid_merge[Merge &\nfilter GTF] hybrid_gtf_out[ ]
stringtie -->|rnaseq| gffcompare gffcompare -->|rnaseq| hybrid_merge hybrid_merge -->|rnaseq| hybrid_gtf_out end
subgraph orf_calling [ORF discovery & calling] star_hybrid[STAR:\nhybrid 2nd pass] ribotish[Ribo-TISH] ribocode[RiboCode] ribotricer[Ribotricer] rpbp[Rp-Bp] price[PRICE] orf_merge[Merge ORF\ncatalogue] orf_catalogue[ ]
star_hybrid -->|riboseq| ribocode ribotish -->|riboseq| orf_merge ribocode -->|riboseq| orf_merge ribotricer -->|riboseq| orf_merge rpbp -->|riboseq| orf_merge price -->|riboseq| orf_merge orf_merge -->|riboseq| orf_catalogue end
subgraph psite_id [P-site identification] ribowaltz[riboWaltz] plastid_psite[plastid\nP-site] plastid_wiggle[plastid\nwiggle] quantify_orf_psite[Quantify ORF\nP-sites] psite_counts_gene[Gene in-frame\nP-sites] psite_orf_out[ ] psite_gene_out[ ]
ribowaltz -->|riboseq| plastid_psite plastid_psite -->|riboseq| plastid_wiggle plastid_wiggle -->|riboseq| quantify_orf_psite plastid_wiggle -->|riboseq| psite_counts_gene quantify_orf_psite -->|riboseq| psite_orf_out psite_counts_gene -->|riboseq| psite_gene_out end
subgraph te [Translational efficiency] te_prep_gene[Gene count\nmatrix] te_prep_orf[ORF count\nmatrix] anota2seq[anota2seq] deltate[DESeq2 deltaTE] dotseq[DOTSeq] _te_merge[ ] te_out[ ]
te_prep_gene -->|riboseq,rnaseq| anota2seq te_prep_gene -->|riboseq,rnaseq| deltate te_prep_orf -->|riboseq,rnaseq| anota2seq te_prep_orf -->|riboseq,rnaseq| deltate te_prep_orf -->|riboseq,rnaseq| dotseq anota2seq -->|riboseq,rnaseq| _te_merge deltate -->|riboseq,rnaseq| _te_merge dotseq -->|riboseq,rnaseq| _te_merge _te_merge -->|riboseq,rnaseq| te_out end
subgraph reporting [Reporting] multiqc_final[MultiQC] report_final[ ]
multiqc_final -->|riboseq,rnaseq| report_final end
%% Inter-section edges equalise -->|riboseq,rnaseq,tiseq| star equalise -->|riboseq| star_hybrid umi_dedup -->|rnaseq| stringtie umi_dedup -->|riboseq| ribotish umi_dedup -->|riboseq| ribotricer umi_dedup -->|riboseq| rpbp umi_dedup -->|riboseq| price umi_dedup -->|riboseq| ribowaltz orf_merge -->|riboseq| ribowaltz salmon_quant -->|rnaseq| te_prep_gene salmon_quant -->|rnaseq| te_prep_orf psite_counts_gene -->|riboseq| te_prep_gene quantify_orf_psite -->|riboseq| te_prep_orf _te_merge -->|riboseq,rnaseq| multiqc_final hybrid_merge -->|annotation| star_hybrid hybrid_merge -->|annotation| ribotish hybrid_merge -->|annotation| ribotricer hybrid_merge -->|annotation| ribocodeCLI command
nf-metro render examples/riboseq_metro.mmd -o riboseq_metro.svg