Announcing WAAFLE 1.5

Microbial community profiling WAAFLE
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WAAFLE 1.5 has been updated to utilize the chocophlan.v202210_202403 SGB database, which is compatible with all bioBakery 4 tools utilizing SGB pangenomes (e.g., MetaPhlAn4 and HUMAnN4, see details MetaPhlAn 4.2.2 release notes). The new WAAFLE database was generated from a curated collection of 168,784 prokaryotic reference and metagenome-assembled genomes clustered into 30,094 species-level genome bins (SGBs). We benchmarked WAAFLE 1.5 and compared its performance to v1.0, finding comparably high sensitivity and specificity for inter-genus LGT events (https://doi.org/10.1038/s41564-024-01881-w). We did observe lower detection of intra-genus events with v1.5, potentially due to extended congeneric overlap between intra-genus SGBs that could not be resolved using current (short-read) assemblies.

What has changed with WAAFLE 1.5:

  • Expansion and improvement of the pangenome database
    • The WAAFLE 1.5 reference database encompasses 168,784 genomes belonging to 30,094 SGBs, a 10-fold expansion compared to WAAFLE 1.0
    • Taxonomy file structure:
      • WAAFLE now uses taxonomic species + SGB as its most specific taxonomic label.
      • Due to changes in SGB organization and taxonomy, the –clade-leaves flag is deprecated.

What has NOT changed in WAAFLE 1.5:

  • The WAAFLE algorithm and expected output.
  • WAAFLE remains compatible with species-level (non-SGB) taxonomy using the appropriate customized database and taxonomy files.

How to make use of WAAFLE 1.5 updates

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Will the release come out soon on the GitHub repo?

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Hi @lucianchauvin ,

Thank you for reaching out to the biobakery lab and apologies for the delay. Here we have the documentation and installation instructions on the new WAAFLE v1.5 release. Please let us know if you run into any issues.

Install WAAFLE and its databases

  • (Option 1) Install the WAAFLE software using PyPi:

    • $ pip install waafle

  • (Option 2) Install the WAAFLE software using conda:

  • (Option 3) Install the WAAFLE software manually:

    • $ git clone https://github.com/biobakery/waafle.git
    • $ python setup.py install
    • See the WAAFLE manual here for other installation options

  • Download the WAAFLE BLAST database and taxonomy file:

  • Unpack the BLAST database:

    • $ tar xzfv chocophlan.v202210_202403.tar.gz

Regards,
Sagun Maharjan