Match this to your CPU's physical cores to speed up the process (e.g., -t 4 ). 3. Focus on Scaffolds vs. Contigs
If you are following a standard microbial genomics curriculum, your "Day 2" workflow typically involves: SPADES-Day2-pc.rar
Running the spades.py command on the cleaned "Day 2" datasets. Match this to your CPU's physical cores to
The most useful feature you should leverage for this topic is the during assembly. 1. Enable the Careful Assembly Mode Contigs If you are following a standard microbial
Set a limit in gigabytes (e.g., -m 8 for 8GB).
When running SPAdes (the executable often found in such packages as spades.py ), the --careful option is a critical feature for small genome projects (like bacteria, which are common in workshops).
Inside your output directory (likely specified in your workshop instructions), you will find two main results: contigs.fasta and scaffolds.fasta .