...
Attempt to assemble with plasmidspades.py which expects to find circularized plasmid type sequences. Command expected to take ~5 ~15 minutes
Code Block language bash title run plasmid spades conda activate GVA-SPAdes plasmidspades.py -t 68 -o unmapped_plasmid -1 SRR4341249-unmapped-vsl.1.fastq -2 SRR4341249-unmapped-vsl.2.fastq
Additionally attempt to assemble with base spades.py command which uses different internal settings to potentially identify different types of novel DNA from our unmapped reads. Command expected to take ~5 take ~15 minutes.
Code Block language bash title run plasmid spades spades.py -t 68 -o unmapped_full -1 SRR4341249-unmapped-vsl.1.fastq -2 SRR4341249-unmapped-vsl.2.fastq
...