Spades-day2-pc.rar

spades.py --careful -1 reads_1.fastq.gz -2 reads_2.fastq.gz -o day2_output 2. Monitor Resource Allocation

Match this to your CPU's physical cores to speed up the process (e.g., -t 4 ). 3. Focus on Scaffolds vs. Contigs

Set a limit in gigabytes (e.g., -m 8 for 8GB). SPADES-Day2-pc.rar

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.

Without it, your final sequence might have small errors that make downstream analysis (like finding genes) more difficult. spades

It reduces the number of mismatches and short indels (insertions/deletions) by running a post-processing tool called MismatchCorrector.

Running the spades.py command on the cleaned "Day 2" datasets. Focus on Scaffolds vs

If you are following a standard microbial genomics curriculum, your "Day 2" workflow typically involves: