Spades-day2-pc.rar

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

spades.py --careful -1 reads_1.fastq.gz -2 reads_2.fastq.gz -o day2_output 2. Monitor Resource Allocation SPADES-Day2-pc.rar

Using tools like Trimmomatic to clean your raw data before assembly. 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 SPADES-Day2-pc.rar

Always prioritize scaffolds.fasta for your "Day 2" analysis. Scaffolds use paired-end read information to bridge gaps between contigs, providing a more complete picture of the genome. Common Workshop Workflow for Day 2

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.