Set a limit in gigabytes (e.g., -m 8 for 8GB).
It reduces the number of mismatches and short indels (insertions/deletions) by running a post-processing tool called MismatchCorrector. SPADES-Day2-pc.rar
Inside your output directory (likely specified in your workshop instructions), you will find two main results: contigs.fasta and scaffolds.fasta . Set a limit in gigabytes (e
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. Set a limit in gigabytes (e.g.
spades.py --careful -1 reads_1.fastq.gz -2 reads_2.fastq.gz -o day2_output 2. Monitor Resource Allocation
Activating the specific environment (e.g., conda activate micro612 ).