Inside your output directory (likely specified in your workshop instructions), you will find two main results: contigs.fasta and scaffolds.fasta .
Using tools like Trimmomatic to clean your raw data before assembly.
spades.py --careful -1 reads_1.fastq.gz -2 reads_2.fastq.gz -o day2_output 2. Monitor Resource Allocation SPADES-Day2-pc.rar
Without it, your final sequence might have small errors that make downstream analysis (like finding genes) more difficult.
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. Inside your output directory (likely specified in your
It reduces the number of mismatches and short indels (insertions/deletions) by running a post-processing tool called MismatchCorrector.
Activating the specific environment (e.g., conda activate micro612 ). Monitor Resource Allocation Without it, your final sequence
Running the spades.py command on the cleaned "Day 2" datasets.