Inside your output directory (likely specified in your workshop instructions), you will find two main results: contigs.fasta and scaffolds.fasta .
Without it, your final sequence might have small errors that make downstream analysis (like finding genes) more difficult. SPADES-Day2-pc.rar
Match this to your CPU's physical cores to speed up the process (e.g., -t 4 ). 3. Focus on Scaffolds vs. Contigs Inside your output directory (likely specified in your
Running the spades.py command on the cleaned "Day 2" datasets. SPAdes is known for being extremely memory-intensive
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.
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).
The most useful feature you should leverage for this topic is the during assembly. 1. Enable the Careful Assembly Mode