sbx_sga (Single Genome Assembly) is a sunbeam extension for isolate QC, assembly, and classification. This pipeline uses Mash for quality control, Shovill for bacterial isolate assembly, CheckM2 and QUAST for assembly QC, MLST for typing, Bakta for annotation, abriTAMR for AMR profiling, and Sylph for taxonomic classification.
- mash_ref: the reference file for running Mash (should be a file ending in
.msh) - checkm_ref: the diamond database for running CheckM2 (should be a file ending in
.dmnd) - bakta_ref: the bakta reference database (should be a directory similar to
.../bakta_db/db/)
More docs.