Spades-day2-pc.rar

Activating the specific environment (e.g., conda activate micro612 ).

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

Without it, your final sequence might have small errors that make downstream analysis (like finding genes) more difficult. 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.

Using tools like Trimmomatic to clean your raw data before assembly. Activating the specific environment (e

Inside your output directory (likely specified in your workshop instructions), you will find two main results: contigs.fasta and scaffolds.fasta .

Set a limit in gigabytes (e.g., -m 8 for 8GB). Enable the Careful Assembly Mode Without it, your

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).