Spades-day2-pc.rar May 2026

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

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

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

Activating the specific environment (e.g., conda activate micro612 ). spades

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

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. Enable the Careful Assembly Mode Set a limit

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