Spades-day2-pc.rar [ Chrome Hot ]

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 ).

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

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

If you are following a standard microbial genomics curriculum, your "Day 2" workflow typically involves: When running SPAdes (the executable often found in

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

spades.py --careful -1 reads_1.fastq.gz -2 reads_2.fastq.gz -o day2_output 2. Monitor Resource Allocation -t 4 ).

Inside your output directory (likely specified in your workshop instructions), you will find two main results: contigs.fasta and scaffolds.fasta .