Example: Atrandi short-read WGS with host removal

This is a full Zorn/Bascet example for Atrandi WGS with Illumina short-read data. See other pages for what each step means - this example is mainly aimed to let you copy-paste something that will work right away

bascetInstance.default <- getBascetBinary()
if(TRUE) {
  #Running locally
  bascetRunner.default <- LocalRunner(mem="50g")
} else {
  #Running on a server with SLURM
  bascetRunner.default <- SlurmRunner(account="hpc2n2026-186", ncpu="10", mem="35g", time="0-14:00:00")
}


####################
### Debarcode
####################

rawmeta <- DetectRawFileMeta("/path/to/fastq")

BascetDebarcode(
  bascetRoot,
  rawmeta,
  chemistry="atrandi-wgs"
)

### Figure out which drops/cells to keep (roughly)
debstat <- PrepareSharding(
  bascetRoot,
  inputName="debarcoded",
  minQuantile=0.95
)

DebarcodedKneePlot(debstat, filename = "kneeplot.pdf")

### Shardify i.e. divide into multiple sets of files for parallel processing. If running local, can also just do 1 shard
BascetShardify(
  debstat,
  numOutputShards = 20
)


####################
### Alignment workflow & host filtering
####################

#We concatenated the Human reference genome, Illumina PhiX, and Xanthomonas, to remove
#these from the reads. Adjust based on what your background DNA is
bwaref <- "/somehwere/human_phi_xantham/all.fa.gz"

### Build BWAMEM2 reference
BascetIndexGenomeBWAMEM2(bwaref)

### Perform alignment
BascetAlignToReference(
  bascetRoot,
  aligner = "BWAMEM2",
  useReference = bwaref
)

### Remove host
BascetFilterAlignment(
    bascetRoot,
    inputName="aligned_cell",
    outputName="aligned_cell_nohost",
    keepMapped=FALSE
)


### Get BAM back to TIRP format
BascetMapTransform(
  bascetRoot,
  inputName="aligned_cell_nohost",
  outputName = "filtered_nohost",
  outFormat="tirp.gz"
)


####################
### Count sketch workflow
####################

BascetRunCountsketch(
  bascetRoot,
  sketchSize=16384,
  inputName="filtered_nohost"
)


####################
### kraken workflow
####################

kraken_db <- "/somewhere/kraken/standard-8"

### Run Kraken2 on each cell
BascetRunKraken(
  bascetRoot,
  inputName="filtered_nohost",
  useKrakenDB = kraken_db
)


####################
### De novo Assembly
####################

### Assemble all genomes
BascetMapCellSKESA(
  bascetRoot,
  inputName = "filtered_nohost"
)


####################
### Analyze contigs
####################

### FastQC
BascetMapCellFASTQC(
  bascetRoot,
  inputName = "filtered_nohost"
)