Spades-day2-pc.rar Online

Using tools like Trimmomatic to clean your raw data before assembly.

The most useful feature you should leverage for this topic is the during assembly. 1. Enable the Careful Assembly Mode

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

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

Without it, your final sequence might have small errors that make downstream analysis (like finding genes) more difficult. Using tools like Trimmomatic to clean your raw

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

Set a limit in gigabytes (e.g., -m 8 for 8GB). Enable the Careful Assembly Mode spades

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