Spades-day2-pc.rar | EXCLUSIVE × VERSION |

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:

Running the spades.py command on the cleaned "Day 2" datasets. SPADES-Day2-pc.rar

The most useful feature you should leverage for this topic is the during assembly. 1. Enable the Careful Assembly Mode

Set a limit in gigabytes (e.g., -m 8 for 8GB). Match this to your CPU's physical cores to

spades.py --careful -1 reads_1.fastq.gz -2 reads_2.fastq.gz -o day2_output 2. Monitor Resource Allocation

It reduces the number of mismatches and short indels (insertions/deletions) by running a post-processing tool called MismatchCorrector. Contigs If you are following a standard microbial

Inside your output directory (likely specified in your workshop instructions), you will find two main results: contigs.fasta and scaffolds.fasta .