One of the most important steps in the Quality control is to remove host genome. You can add any number of genomes to be removed.
We recommend you to use genomes where repetitive sequences are masked. See here for more details human genome.
Limitation: Hybrid assembly of long and short reads is supported with spades and metaSpades. However metaSpades needs a paired-end short-read library.
The path of the (preprocessed) long reads should be added manually to the the sample table under a new column heading 'longreads'.
In addition the type of the long reads should be defined in the config file: longread_type one of ["pacbio", "nanopore", "sanger", "trusted-contigs", "untrusted-contigs"]
../advanced/qc ../advanced/assembly