It reduces the number of mismatches and short indels (insertions/deletions) by running a post-processing tool called MismatchCorrector.
Running the spades.py command on the cleaned "Day 2" datasets.
Activating the specific environment (e.g., conda activate micro612 ). SPADES-Day2-pc.rar
Set a limit in gigabytes (e.g., -m 8 for 8GB).
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). It reduces the number of mismatches and short
Always prioritize scaffolds.fasta for your "Day 2" analysis. Scaffolds use paired-end read information to bridge gaps between contigs, providing a more complete picture of the genome. Common Workshop Workflow for Day 2
spades.py --careful -1 reads_1.fastq.gz -2 reads_2.fastq.gz -o day2_output 2. Monitor Resource Allocation Set a limit in gigabytes (e
Using tools like Trimmomatic to clean your raw data before assembly.