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).
Inside your output directory (likely specified in your workshop instructions), you will find two main results: contigs.fasta and scaffolds.fasta . SPADES-Day2-pc.rar
The most useful feature you should leverage for this topic is the during assembly. 1. Enable the Careful Assembly Mode When running SPAdes (the executable often found in
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. Running the spades
Running the spades.py command on the cleaned "Day 2" datasets.
It reduces the number of mismatches and short indels (insertions/deletions) by running a post-processing tool called MismatchCorrector.
Without it, your final sequence might have small errors that make downstream analysis (like finding genes) more difficult.
