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 .

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

Without it, your final sequence might have small errors that make downstream analysis (like finding genes) more difficult. Inside your output directory (likely specified in your

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 Always prioritize scaffolds

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 ).

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).