spades.py --careful -1 reads_1.fastq.gz -2 reads_2.fastq.gz -o day2_output 2. Monitor Resource Allocation
Activating the specific environment (e.g., conda activate micro612 ). SPADES-Day2-pc.rar
It reduces the number of mismatches and short indels (insertions/deletions) by running a post-processing tool called MismatchCorrector. spades
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). your "Day 2" workflow typically involves:
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 curriculum, your "Day 2" workflow typically involves: