SampleData[Contigs]

Artifact containing contigs, organized as one FASTA file per sample. Contigs are contiguous sequences of DNA that are assembled from overlapping reads.

Artifact Format

class ContigSequencesDirFmt(model.DirectoryFormat):
    sequences = model.FileCollection(
        r'[^\.].+_contigs.(fasta|fa)$',
        format=DNAFASTAFormat
    )

Expected Folder Structure

data
├── <sample_id>_contigs.fa
⋮
└── <sample_id>_contigs.fa

Where to find SampleData[Contigs]

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

As Input

• qiime assambly index-contigs
• qiime assambly evaluate-contigs
• qiime moshpit eggnog-diamond-search
• qiime moshpit bin-contigs-metabat
• qiime moshpit classify-kraken2 # TODO: Link to md page

As Output

• qiime assambly assemble-megahit
• qiime assambly assemble-spades

As Input and Output

• qiime assambly partition-contigs
• qiime assambly collate-contigs