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 SPADES-Day2-pc.rar

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). spades

If you are following a standard microbial genomics curriculum, your "Day 2" workflow typically involves: SPADES-Day2-pc.rar

The most useful feature you should leverage for this topic is the during assembly. 1. Enable the Careful Assembly Mode