WAAFLE

Workflow to Annotate Assemblies and Find LGT Events

What is WAAFLE?

WAAFLE (Workflow to Annotate Assemblies and Find LGT Events) is a tool for detecting potential horizontal gene transfer (HGT) events, specifically lateral gene transfer (LGT), from metagenomic assemblies. It analyzes contigs from metagenomes and identifies genes or gene segments that appear to originate from a different lineage than the surrounding genomic context.

WAAFLE answers the question: “Which genes in this metagenome may have been transferred between different microbial lineages?”

When to Use WAAFLE

Use WAAFLE when you want to:

  • Detect lateral gene transfer (LGT) events in metagenome-assembled contigs
  • Identify genes that appear to have been transferred across kingdoms or phyla
  • Characterize mobile genetic elements in microbiome data

Installation

Via conda

conda create -n waafle -c biobakery waafle
conda activate waafle

Via pip

pip install waafle

Dependencies

  • BLAST+ — for gene annotation
  • bowtie2 — for read-level analysis

Basic Usage

WAAFLE takes assembled metagenomic contigs as input.

Step 1: Gene annotation with BLAST

waafle_search \
  contigs.fna \
  /path/to/waafle_db/waafledb \
  --out contigs.bls

Step 2: Find LGT events

waafle_orgscorer \
  contigs.fna \
  contigs.bls \
  /path/to/waafle_db/waafle_taxonomy.tsv \
  --out-lgt contigs_lgt.tsv \
  --out-no-lgt contigs_no_lgt.tsv \
  --out-unclassified contigs_unclassified.tsv

Output Files

File Contents
*_lgt.tsv Contigs with detected LGT events
*_no_lgt.tsv Contigs with no LGT detected (single-clade)
*_unclassified.tsv Contigs that could not be classified

LGT output columns

Column Description
CONTIG_NAME Name of the contig
LENGTH Contig length (bp)
CLADE_A Donor clade assignment
CLADE_B Recipient clade assignment
LGT_REGIONS Genomic coordinates of transfer

Tips & Gotchas

Tip

Assembly quality matters — WAAFLE works best with longer, high-quality contigs (>1000 bp). Short contigs may not have enough context for reliable LGT detection.

Warning

False positives — Chimeric assemblies (assembly errors that join sequences from different organisms) can be misidentified as LGT. Validate candidates with additional methods.

Tip

Taxonomic resolution — WAAFLE works at various taxonomic levels. Inter-kingdom transfers (e.g., bacteria → archaea) are more reliable signals than intra-genus transfers.

Further Reading