03_ASSEMBLIES

Each sample will be assembled separately. This decision was made after much deliberation. The inability to coassemble large metagenome datasets is a burden to sample comparison downstream in some cases, but hopefully this can be overcome at the various levels of information we are seeking.

We employ MEGAHIT for the assembly. I have elected to process each sample separately in a loop, but this could perhaps be better optimized for instance if I were to do this on SAGA, by cutting it into several parallel jobs instead of one large job as I do here.

# On kjempefuru:
AMOR_2019_path='/export/dahlefs/work/Shotgun/Metagenomes_chimneys_2019/01_QC'
AMOR_2020_path='/export/dahlefs/work/Metagenomes_chimneys_2020_workfolder/02_HUMAN_Decontam/'