Assembled sequences annotation

In this section we will focus on AMR gene annotation of assembled sequences using the plugin q2-amrfinderplus.

Fetch database¶

First we need to fetch the AMRFinderPlus database with the fetch-amrfinderplus-db action. It automatically downloads the newest version of the database.

qiime amrfinderplus fetch-amrfinderplus-db \
    --o-amrfinderplus-db amrfinderplus-db \
    --verbose

Predict genes¶

To annotate assembled sequences with AMR genes, we first have to perform gene prediction. This can be done with the action predict-prodigal from the package q2-annotate.

mosh annotate predict-genes-prodigal \
    --i-seqs contigs.qza \
    --o-loci loci_contigs.qza \
    --o-genes genes_contigs.qza \
    --o-proteins proteins_contigs.qza \
    --verbose

Annotate contigs¶

The database and the predicted proteins and loci can now be used to annotate the contigs, with the annotate action. The action uses assembled sequences (SampleData[MAGs], SampleData[Contigs] and FeatureData[MAG]), proteins (GenomeData[Proteins]) and loci (GenomeData[Loci]) as inputs. It is recommended to run the annotation in the combined mode with sequences, predicted proteins and predicted loci, as this is the most sensitive. The outputs are the amr annotations in form of a TXT file and the detected AMR gene and protein sequences in FASTA format. Also provided are annotations called “all mutations”, they contain the genotypes at all locations screened for point mutations if an organism is specified with the organism parameter. For this run the all mutations output will be empty. For more information about how to run AMRFinderPlus and interpret the results please consult the AMRFinderPlus documentation.

qiime amrfinderplus annotate \
    --i-amrfinderplus-db amrfinderplus-db.qza \
    --i-sequences contigs.qza \
    --i-proteins proteins_contigs.qza \
    --i-loci loci_contigs.qza \
    --o-amr-annotations amrfinderplus_annotations.qza \
    --o-amr-all-mutations amrfinderplus_all_mutations.qza \
    --o-amr-genes amrfinderplus_genes.qza \
    --o-amr-proteins amrfinderplus_proteins.qza \
    --verbose

Tabulate annotations¶

With the tabulate visualizer of the q2-metadata plugin it is possible to generate a tabular combined view of the AMR annotations.

qiime metadata tabulate \
    --m-input-file amrfinderplus_annotations.qza \
    --o-visualization amrfinderplus_annotations_tabulated.qzv

Your visualization should look similar to this one.