nf-core/rnaseq

nf-core pipelines

RNA-seq analysis with multiple aligner and quantification routes (STAR/RSEM, STAR/Salmon, HISAT2, Salmon pseudo-alignment, Kallisto). GitHub

Mermaid source

examples/rnaseq_auto.mmd

%%metro title: nf-core/rnaseq
%%metro logo: examples/nf-core-rnaseq_logo_light.png | examples/nf-core-rnaseq_logo_dark.png
%%metro style: dark
%%metro line: star_rsem | Aligner: STAR, Quantification: RSEM | #0570b0
%%metro line: star_salmon | Aligner: STAR, Quantification: Salmon (default) | #2db572
%%metro line: hisat2 | Aligner: HISAT2, Quantification: None | #f5c542
%%metro line: pseudo_salmon | Pseudo-aligner: Salmon, Quantification: Salmon | #e63946
%%metro line: pseudo_kallisto | Pseudo-aligner: Kallisto, Quantification: Kallisto | #7b2d3b
%%metro legend: bl
%%metro logo_scale: 0.6

graph LR
    subgraph preprocessing [Pre-processing]
        cat_fastq[cat fastq]
        fastqc_raw[FastQC]
        infer_strandedness[infer strandedness]
        umi_tools_extract[UMI-tools extract]
        fastp[FastP]
        trimgalore[Trim Galore!]
        fastqc_trimmed[FastQC]
        bbsplit[BBSplit]
        sortmerna[SortMeRNA]

        cat_fastq -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| fastqc_raw
        fastqc_raw -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| infer_strandedness
        infer_strandedness -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| umi_tools_extract

        umi_tools_extract -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| fastp
        umi_tools_extract -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| trimgalore
        fastp -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| fastqc_trimmed
        trimgalore -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| fastqc_trimmed

        fastqc_trimmed -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| bbsplit
        bbsplit -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| sortmerna
    end

    subgraph genome_align [Genome alignment & quantification]
        star[STAR]
        hisat2_align[HISAT2]
        rsem[RSEM]
        salmon_quant[Salmon]
        umi_tools_dedup[UMI-tools dedup]

        star -->|star_rsem| rsem
        star -->|star_salmon| umi_tools_dedup
        umi_tools_dedup -->|star_salmon| salmon_quant
        hisat2_align -->|hisat2| umi_tools_dedup
    end

    subgraph postprocessing [Post-processing]
        samtools[SAMtools]
        picard[Picard]
        bedtools[BEDTools]
        bedgraph[bedGraphToBigWig]
        stringtie[StringTie]

        samtools -->|star_salmon,star_rsem,hisat2| picard
        picard -->|star_salmon,star_rsem,hisat2| bedtools
        bedtools -->|star_salmon,star_rsem,hisat2| bedgraph
        bedgraph -->|star_salmon,star_rsem,hisat2| stringtie
    end

    subgraph pseudo_align [Pseudo-alignment & quantification]
        salmon_pseudo[Salmon]
        kallisto[Kallisto]
        multiqc_pseudo[MultiQC]

        salmon_pseudo -->|pseudo_salmon| multiqc_pseudo
        kallisto -->|pseudo_kallisto| multiqc_pseudo
    end

    subgraph qc_report [Quality control & reporting]
        rseqc[RSeQC]
        preseq[Preseq]
        qualimap[Qualimap]
        dupradar[dupRadar]
        deseq2_pca[DESeq2 PCA]
        kraken2[Kraken2/Bracken]
        multiqc_final[MultiQC]

        rseqc -->|star_salmon,star_rsem,hisat2| preseq
        preseq -->|star_salmon,star_rsem,hisat2| qualimap
        qualimap -->|star_salmon,star_rsem,hisat2| dupradar
        dupradar -->|star_salmon,star_rsem,hisat2| deseq2_pca
        deseq2_pca -->|star_salmon,star_rsem,hisat2| kraken2
        kraken2 -->|star_salmon,star_rsem,hisat2| multiqc_final
    end

    %% Inter-section edges
    sortmerna -->|star_salmon,star_rsem| star
    sortmerna -->|hisat2| hisat2_align
    sortmerna -->|pseudo_salmon| salmon_pseudo
    sortmerna -->|pseudo_kallisto| kallisto
    salmon_quant -->|star_salmon| samtools
    rsem -->|star_rsem| samtools
    umi_tools_dedup -->|hisat2| samtools
    stringtie -->|star_salmon,star_rsem,hisat2| rseqc

CLI command

nf-metro render examples/rnaseq_auto.mmd -o rnaseq_auto.svg

Rendered map