De novo assembly

First set up your Zorn/Bascet work directory as before.

Assembly can then performed using SKESA, via the MapCell system:

(SLURM-compatible step)

### Assemble all genomes
BascetMapCellSKESA(
  bascetRoot,
  inputName = "filtered",
  outputName = "contigs"
)

This produce contigs for each cell, all grouped together in “skesa”. Note that both skesa and spades only assembles cells for which there are sufficient number of reads.

#TODO extract an individual genome

#TODO QUAST for QC etc