Version Compatibility

Reference examples tested with: FastQC 0.12+, MEGAHIT 1.2+, SPAdes 3.15+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Short-Read Assembly

"Assemble a genome from Illumina reads" → Build a de novo assembly from short paired-end reads using de Bruijn graph algorithms with multiple k-mer sizes.

• CLI: spades.py -1 R1.fq.gz -2 R2.fq.gz -o output

SPAdes Overview

SPAdes (St. Petersburg genome Assembler) uses de Bruijn graph approach with multiple k-mer sizes for robust assembly.