SampleData[MAGs]

SampleData[MAGs] represents artifacts containing MAGs, organized by sample in folders. Individual MAGs are DNAFASTAFormat files. The MANIFEST is a table specifying the relationship MAGs and samples.

Artifact Format

class MultiMAGSequencesDirFmt(MultiFASTADirectoryFormat):
    sequences = model.FileCollection(r'.+\.(fa|fasta)$', format=DNAFASTAFormat)
    manifest = model.File('MANIFEST', format=MultiMAGManifestFormat)

Expected Folder Structure

data
├── MANIFEST
├── <sample_id>
│   ├── <mag_id>.fasta
│   ⋮
│   └── <mag_id>.fasta
⋮
└── <sample_id>
    ├── <mag_id>.fasta
    ⋮
    └── <mag_id>.fasta

Where to find SampleData[MAGs]

• See Generate MAGs from reads tutorial for a full example.
• Below we list actions in q2-moshpit that have this semantic type as output or input.

As Input

• qiime moshpit dereplicate-mags
• qiime moshpit evaluate-busco

As Output

• qiime moshpit bin-contigs-metabat