spades.py --careful -1 reads_1.fastq.gz -2 reads_2.fastq.gz -o day2_output 2. Monitor Resource Allocation
If you are following a standard microbial genomics curriculum, your "Day 2" workflow typically involves: SPADES-Day2-pc.rar
It reduces the number of mismatches and short indels (insertions/deletions) by running a post-processing tool called MismatchCorrector. spades
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
Set a limit in gigabytes (e.g., -m 8 for 8GB).
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.