Co-binning
Co-binning with sub-groups
In this new version, Atlas uses binning with co-abundance as default.
While binning each sample individually is faster, using co-abundance for binning, by quantifying the coverage of contigs across multiple samples provides valuable insights about contig co-variation.
Starting with version 2.18, atlas places every sample in a single BinGroup and defaults to vamb as the binner unless there are very few samples. For fewer than 8 samples, metabat is the default binner.
The defaults are fine except when you have many samples (>150) where atlas gives a warning that you should put sour samples in more than one bin group.
Note
Previously each sample was put in its own BinGroup optimized for single-sample binning.
Running vamb in those versions would consider all samples, regardless of their BinGroup.
Hence updating to v2.18 might cause errors if using a sample.tsv file from an older Atlas version.
You can resolve this by assigning a unique BinGroup to each sample.
Full Changelog: v2.17.2...v2.18.0