Inside your output directory (likely specified in your workshop instructions), you will find two main results: contigs.fasta and scaffolds.fasta .
If you are following a standard microbial genomics curriculum, your "Day 2" workflow typically involves: SPADES-Day2-pc.rar
Using tools like Trimmomatic to clean your raw data before assembly. Inside your output directory (likely specified in your
Activating the specific environment (e.g., conda activate micro612 ). 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
Without it, your final sequence might have small errors that make downstream analysis (like finding genes) more difficult.
spades.py --careful -1 reads_1.fastq.gz -2 reads_2.fastq.gz -o day2_output 2. Monitor Resource Allocation
