Minimum MAG length
Bérénice BatutIn dRep, the set of Metagenome-Assembled Genomes (MAGs) undergoes quality filtering before any comparisons are performed. This critical step ensures that only high-quality genomes are retained for downstream analysis, improving both accuracy and computational efficiency.
One of the first steps in quality filtering is length-based filtering. Genomes that do not meet the minimum length threshold are filtered out upfront. This avoids unnecessary CheckM computations and ensures that only sufficiently large genomes are processed.
Important Note: All genomes must contain at least one predicted Open Reading Frame (ORF). Without an ORF, CheckM may stall during processing. To prevent this, a minimum genome length of 10,000 base pairs (bp) is recommended.
The default minimum length threshold in dRep is 50,000 bp. This threshold strikes a balance between computational efficiency and genome quality, ensuring that only meaningful and sufficiently complete genomes are included in the de-replication process.