Version Compatibility

Reference examples tested with: QUAST 5.2+, SPAdes 3.15+, minimap2 2.26+, pandas 2.2+, samtools 1.19+

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

• Python: pip show <package> then help(module.function) to check signatures
• 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.

Metagenome Assembly

"Assemble genomes from my metagenome data" → Reconstruct individual microbial genomes (MAGs) from mixed community sequencing reads using metagenome-aware assemblers and binning.

• CLI: flye --meta --nano-raw reads.fq (long-read), metaspades.py -1 R1.fq -2 R2.fq (short-read)

Overview

Metagenome assembly reconstructs genomes from mixed microbial communities. Long reads enable recovery of complete circular genomes and resolution of strain-level differences.