Introduction Usage Parameters Output

Introduction

This document describes the output produced by ncrnannotator. All paths are relative to the --outdir directory specified at runtime.

Pipeline overview

ncrnannotator runs the following steps:

  1. FILTER_RFAM_CM — filter Rfam covariance models to clade-specific accessions (skipped in mgnify-assembly and full modes)
  2. GENOME_CHUNK — split genome into non-overlapping windows for parallel processing
  3. CMSEARCH — search each chunk against Rfam covariance models using Infernal
  4. PARSE_RFAM — consolidate results, remove overlapping hits, apply GA score thresholds
  5. RFAM_TO_FORMATS — convert hits to GTF, GFF3, and BED annotation files
  6. MultiQC — aggregate software versions and pipeline metrics into a report

Output directories

rfam/

Intermediate Rfam files published for inspection and reuse.

Output files
  • rfam/
    • rfam_filtered.cm — Rfam covariance model file filtered to clade-specific accessions (not present in mgnify-assembly or full mode)
    • rfam_hits.tsv — Tab-separated table of all final ncRNA hits after overlap removal and score filtering

rfam_hits.tsv format

Column Description
seqname Sequence name from the input FASTA
start Hit start position (1-based)
end Hit end position (1-based, inclusive)
strand Strand (+ or -)
score Infernal bit score
evalue E-value
query_name Rfam model name (e.g. U1, 5S_rRNA)
accession Rfam accession (e.g. RF00003)
biotype Ensembl-style biotype (e.g. snRNA, snoRNA, rRNA, lncRNA)

annotation/

Final annotation files ready for use in genome browsers and downstream analysis.

Output files
  • annotation/
    • annotation.gtf — GTF v2.2 annotation with gene/transcript/exon features
    • annotation.gff3 — GFF3 annotation with gene/ncRNA/exon hierarchy
    • annotation.bed — 6-column BED file (0-based start coordinates)

GTF format

Ensembl-style GTF with three feature types per hit: gene, transcript, exon. Key attributes:

  • gene_id — sequential identifier (e.g. rfam_gene_000001)
  • gene_name — Rfam model name
  • gene_biotype — Ensembl biotype (e.g. snRNA, snoRNA, rRNA)
  • rfam_accession — Rfam family accession

GFF3 format

Standard GFF3 with gene → ncRNA (or biotype-specific type) → exon hierarchy. Feature types follow Sequence Ontology conventions.

BED format

6-column BED (chrom, chromStart, chromEnd, name, score, strand). Start is 0-based. Score is clamped to 0–1000.

multiqc/

Output files
  • multiqc/
    • multiqc_report.html — standalone HTML report viewable in any browser
    • multiqc_data/ — parsed statistics from all pipeline steps
    • multiqc_plots/ — static images from the report

MultiQC aggregates software versions and pipeline metrics into a single report.

pipeline_info/

Output files
  • pipeline_info/
    • execution_report.html — Nextflow execution report (resource usage per task)
    • execution_timeline.html — timeline of all tasks
    • execution_trace.txt — tab-separated trace of all tasks
    • nf_core_ncrnannotator_software_mqc_versions.yml — software versions used

Nextflow provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.

Biotype reference

The following biotypes are assigned based on Rfam model names and seed classifications:

Biotype Examples
snRNA U1, U2, U4, U5, U6, U11, U12
snoRNA SNORD, SNORA families
scaRNA scaRNA families
rRNA 5S_rRNA, 5_8S_rRNA, SSU_rRNA_eukarya, LSU_rRNA_eukarya
rRNA (prokaryotic, mgnify-assembly only) SSU_rRNA_bacteria, LSU_rRNA_archaea, etc.
tRNA tRNA families
pre_miRNA miRNA precursors
lncRNA Long non-coding RNA
SRP_RNA Signal recognition particle RNA
RNase_P_RNA RNase P families
vault_RNA Vault RNA
Y_RNA Y RNA families
ribozyme Ribozyme families
antisense_RNA Antisense RNA
ncRNA Other non-coding RNA (default)
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