Spades-day2-pc.rar -

Running the spades.py command on the cleaned "Day 2" datasets.

Set a limit in gigabytes (e.g., -m 8 for 8GB). SPADES-Day2-pc.rar

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

Match this to your CPU's physical cores to speed up the process (e.g., -t 4 ). 3. Focus on Scaffolds vs. Contigs Match this to your CPU's physical cores to

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).

Without it, your final sequence might have small errors that make downstream analysis (like finding genes) more difficult.

SPAdes is known for being extremely memory-intensive. A useful practice during "Day 2" exercises is explicitly limiting its resource usage to prevent your PC from crashing.