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Genome annotation tools

Source: vignettes/genome_annotation.Rmd
genome_annotation.Rmd

QUAST

First run QUAST on all the cells: (SLURM-compatible step)

BascetMapCell(
  bascetRoot,
  withfunction = "_quast",
  inputName = "skesa",  #or other source of contigs
  outputName = "quast"
)

Then aggregate the results for visualization. This example caches the result to speed up reloading; this is optional

quast_aggr <- BascetCacheComputation(bascetRoot,"cache_quast",MapListAsDataFrame(BascetAggregateMap(
  bascetRoot,
  "quast",
  aggr.quast
)))

Abricate

First run Abricate on all the cells. The NCBI database is used by default. See ListDatabaseAbricate() for a list of other databases

(SLURM-compatible step)

BascetMapCellAbricate(
  bascetRoot,
  inputName = "skesa"  #or other source of contigs
)

Then aggregate the results for visualization. This example caches the result to speed up reloading; this is optional

quast_aggr <- BascetCacheComputation(bascetRoot,"cache_abricate",MapListAsDataFrame(BascetAggregateMap(
  bascetRoot,
  "abricate",
  aggr.abricate
)))

Bakta

First download a database:

DownloadDatabaseBakta(
  dbdir="~/bakta",  #create directory before running command
  dbtype="light"
)

You can run then run Bakta on all cells: (SLURM-compatible step)

### ....
BascetMapCellBakta(
  bascetRoot,
  db = "~/bakta",
  inputName = "skesa",  #or other source of contigs
)

Then aggregate the results for visualization. This example caches the result to speed up reloading; this is optional

quast_aggr <- BascetCacheComputation(bascetRoot,"cache_bakta",MapListAsDataFrame(BascetAggregateMap(
  bascetRoot,
  "bakta",
  aggr.bakta
)))