Output

Repeat Pipeline Output Guide

This guide describes all outputs generated by the Ensembl genes repeat annotation pipeline, including file formats, locations and interpretation.

Table of Contents

  1. Output Directory Structure

  2. Module Outputs

  3. File Formats

  4. Cached Outputs

  5. Version Tracking

  6. Interpreting Results

Output Directory Structure

Standard Layout

${params.outdir}/
├── ${meta.gca}/
│   ├── rm_library/                  # Downloaded RepeatModeler library
│   ├── repeatmasker/                # RepeatMasker results
│   ├── red/                         # RED repeat detection results
│   ├── repeat_statistics/           # Repeat annotation statistics
│   ├── reports/                     # Summary reports
│   └── versions.yml                 # Software versions
│
└── pipeline_info/
    ├── execution_report.html
    ├── execution_timeline.html
    └── execution_trace.txt

Cache Directory Structure

${params.cacheDir}/
├── ${meta.gca}/
│   ├── repeatmodeler/
│   ├── repeatmasker/
│   └── red/
│
└── repeat_libraries/

Module Outputs

CHECK_AND_DOWNLOAD_RMLIBRARY

Published to: ${params.outdir}/${meta.gca}/rm_library/

Files

  • ${meta.gca}.repeatmodeler.fa

  • versions.yml

Description

Downloads the RepeatModeler repeat library from the supplied URL after validating that the resource exists.

Typical Output

rm_library/
├── GCA_XXXXXXXXX.X.repeatmodeler.fa
└── versions.yml

CHECK_AND_DOWNLOAD_DFAM

Published to: ${params.outdir}/${meta.gca}/dfam/

Files

  • Dfam repeat library

  • versions.yml

Description

Downloads and prepares the selected Dfam repeat library for downstream annotation.

RUN_REPEATMASKER

Published to: ${params.outdir}/${meta.gca}/repeatmasker/

Typical Files

  • Masked genome FASTA

  • .out

  • .tbl

  • .cat.gz

  • Annotation files

  • versions.yml

Description

Runs RepeatMasker using the configured repeat library and produces masked genome sequences together with detailed repeat annotations.

RUN_RED

Published to: ${params.outdir}/${meta.gca}/red/

Typical Files

  • Repeat coordinates

  • Soft-masked genome

  • Summary statistics

  • versions.yml

Description

Detects repetitive regions using RED without relying on a predefined repeat library.

Repeat Statistics

Published to: ${params.outdir}/${meta.gca}/repeat_statistics/

Typical Outputs

  • Repeat counts

  • Repeat coverage

  • Repeat class summaries

  • Summary reports

These statistics summarise the repeat content identified across the genome assembly.

File Formats

FASTA

Used for:

  • RepeatModeler libraries

  • Masked genome assemblies

GFF/BED

Used for genomic repeat coordinates.

Typical fields include:

  • sequence

  • start

  • end

  • strand

  • repeat class

  • repeat family

RepeatMasker Output

Typical files include:

  • .out

  • .tbl

  • .cat.gz

These contain the detailed RepeatMasker annotation and summary statistics.

YAML

Every module generates a versions.yml file describing the software versions used during execution.

Example:

CHECK_AND_DOWNLOAD_RMLIBRARY:
  wget: 1.24

RUN_REPEATMASKER:
  RepeatMasker: 4.1.x

RUN_RED:
  RED: 2.x

Cached Outputs

The pipeline caches expensive resources whenever possible.

Examples include:

  • downloaded RepeatModeler libraries

  • downloaded Dfam libraries

  • RepeatMasker intermediate files

  • RED intermediate files

Caching avoids repeated downloads and unnecessary recomputation.

Version Tracking

Every module generates a versions.yml file recording the versions of the software used during execution.

Typical tools include:

  • RepeatMasker

  • RepeatModeler

  • RED

  • wget

  • Perl

  • Python

These files support reproducibility and troubleshooting.

Interpreting Results

RepeatMasker

The RepeatMasker output provides:

  • repeat family assignments

  • repeat class assignments

  • genomic coordinates

  • percentage divergence from the consensus sequence

Higher repeat coverage generally indicates a more repetitive genome.

RED

RED identifies repetitive regions independently of known repeat libraries.

Comparing RED and RepeatMasker results can help identify:

  • novel repeat content

  • lineage-specific repeats

  • gaps in curated repeat libraries

Output Checklist

After pipeline completion verify that:

  • RepeatModeler libraries were downloaded successfully.

  • RepeatMasker completed without errors.

  • RED completed successfully.

  • Repeat statistics were generated.

  • All expected output directories are present.

  • versions.yml files exist.

  • Pipeline execution reports were produced.

Quick Reference

Module

Primary Output

Location

CHECK_AND_DOWNLOAD_RMLIBRARY

RepeatModeler library

${params.outdir}/${meta.gca}/rm_library/

CHECK_AND_DOWNLOAD_DFAM

Dfam library

${params.outdir}/${meta.gca}/dfam/

RUN_REPEATMASKER

Repeat annotations

${params.outdir}/${meta.gca}/repeatmasker/

RUN_RED

RED repeat annotations

${params.outdir}/${meta.gca}/red/

Repeat Statistics

Summary reports

${params.outdir}/${meta.gca}/repeat_statistics/

All modules

versions.yml

${params.outdir}/${meta.gca}/

Next Steps