The most useful feature you should leverage for this topic is the during assembly. 1. Enable the Careful Assembly Mode
Activating the specific environment (e.g., conda activate micro612 ). SPADES-Day2-pc.rar
Inside your output directory (likely specified in your workshop instructions), you will find two main results: contigs.fasta and scaffolds.fasta . The most useful feature you should leverage for
Using tools like Trimmomatic to clean your raw data before assembly. Inside your output directory (likely specified in your
Without it, your final sequence might have small errors that make downstream analysis (like finding genes) more difficult.
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).
spades.py --careful -1 reads_1.fastq.gz -2 reads_2.fastq.gz -o day2_output 2. Monitor Resource Allocation
