Using tools like Trimmomatic to clean your raw data before assembly.
Set a limit in gigabytes (e.g., -m 8 for 8GB). SPADES-Day2-pc.rar
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). Using tools like Trimmomatic to clean your raw
spades.py --careful -1 reads_1.fastq.gz -2 reads_2.fastq.gz -o day2_output 2. Monitor Resource Allocation SPADES-Day2-pc.rar
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.
Without it, your final sequence might have small errors that make downstream analysis (like finding genes) more difficult.