MAG annotation

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

To annotate MAGs with ARGs from CARD we can use the annotate-mags-card action. We can choose from two different alignment tools. While DIAMOND is faster, BLAST is more sensitive. By default, annotations include perfect matches (100% sequence identity) and strict matches (>95% sequence identity). Loose matches (>95% sequence identity) are optional and can be added if preferred. Please refer to the RGI documentation for more information about RGI and the perfect/strict/loose matches. The outputs include the annotations in form of TXT files and as a feature table.

qiime rgi annotate-mags-card \
    --i-mag mags.qza \
    --i-card-db card_db.qza \
    --p-alignment-tool DIAMOND \
    --o-amr-annotations rgi_annotations_mags.qza \
    --o-feature-table rgi_feature_table_mags.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 rgi_annotations_mags.qza \
  --o-visualization rgi_annotations_mags_tabulated.qzv

Your visualization should look similar to this one.