1.0.0

First release of nf-core/rnastructurome, which analyses chemical high-throughput RNA structure-probing data and predicts RNA secondary structures from it. The pipeline covers SHAPE and DMS chemistries read out by either the RT-stop or mutational profiling (MaP) principle, and runs in two modes depending on the reference: a genome route aligned with STAR and a transcriptome route aligned with Bowtie/Bowtie2.

Added

• Single- and paired-end FASTQ input, with re-sequenced samples concatenated automatically.
• Read quality control with FastQC before and after adapter and quality trimming with Cutadapt.
• Optional UMI extraction and UMI-aware deduplication with UMI-tools; position-based duplicate removal with SAMtools markdup is available but off by default.
• Reference genomes and annotations downloaded automatically from Ensembl, falling back to NCBI for bacteria, viruses and other organisms Ensembl does not cover, or supplied directly as local files.
• Genome-route alignment with STAR, and transcriptome-route alignment with Bowtie for RT-stop and Bowtie2 for MaP.
• BAM sorting, indexing and alignment statistics with SAMtools.
• Per-base reactivity counting with rf-count, tallying mutations for MaP and RT-stops for RT-stop on transcript coordinates.
• An alternative genome-coordinate counting path with rf-count-genome, resolving library strandedness with BEDOPS and RSeQC and extracting per-transcript reactivity with rf-rctools.
• Reactivity normalisation with rf-norm, pairing treated, untreated and denatured samples automatically and selecting scoring and normalisation methods from the controls present.
• Replicate reproducibility QC with rf-correlate, reporting pairwise Pearson and Spearman correlation of reactivity profiles.
• RNA secondary structure prediction across grouped replicates with rf-fold, using chemistry- and reagent-aware folding defaults.
• Reactivity, Shannon entropy and base-pair arc tracks in transcript and genome coordinates, generated with rf-wiggle and UCSC wigToBigWig.
• 2D structure diagrams coloured by reactivity, drawn with ViennaRNA RNAplot and, where a template model exists for the RNA type, with R2DT alongside them. R2DT is container-only, so -profile conda draws with ViennaRNA alone.
• RMDB-compatible RDAT export combining per-transcript reactivity and structure.
• Optional folding calibration against known structures with rf-jackknife, which tunes the slope and intercept passed to rf-fold.
• Optional structural-element extraction of high-confidence, low-reactivity and low-Shannon motifs with rf-structextract.
• Optional structure-accuracy evaluation with rf-eval, reporting AUROC, DSCI and the unpaired coefficient against an automatic rotation baseline.
• Aggregated quality-control report with MultiQC, including alignment, reactivity and replicate-correlation summaries.
• Test profiles for the genome route, the transcriptome route, a prokaryote run with jackknife calibration, and a full-size rice DMS-MaPseq dataset.