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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How to install the WAAFLE 1.5 BLAST database and taxonomy file
- Download the WAAFLE BLAST database and taxonomy file:
- Unpack the BLAST database:
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$ tar xzfv chocophlan.v202210_202403.tar.gz
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Follow these steps to run WAAFLE