If you are following a standard microbial genomics curriculum, your "Day 2" workflow typically involves:
Set a limit in gigabytes (e.g., -m 8 for 8GB).
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-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. If you are following a standard microbial genomics
It reduces the number of mismatches and short indels (insertions/deletions) by running a post-processing tool called MismatchCorrector.
Match this to your CPU's physical cores to speed up the process (e.g., -t 4 ). 3. Focus on Scaffolds vs. Contigs Without it, your final sequence might have small
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