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).
It reduces the number of mismatches and short indels (insertions/deletions) by running a post-processing tool called MismatchCorrector. SPADES-Day2-pc.rar
Activating the specific environment (e.g., conda activate micro612 ). When running SPAdes (the executable often found in
Running the spades.py command on the cleaned "Day 2" datasets. SPADES-Day2-pc.rar
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.