Choosing the right read strategy for complete, contiguous microbial genomes in 2026.
Closing a microbial genome is no longer a heroic effort — but choosing the wrong read strategy still wastes time and budget. The decision comes down to what you need from the assembly.
Short reads: accuracy and throughput
Illumina and MGI short reads deliver the lowest per-base error and the highest throughput, making them ideal for SNP calling and large cohorts. Their limitation is repeats: regions longer than the read length collapse, fragmenting the assembly.
Long reads: contiguity
PacBio HiFi and Oxford Nanopore reads span repeats and structural variants, routinely producing single-contig bacterial chromosomes and resolving plasmids that short reads miss entirely.
For most microbial genomes in 2026, a hybrid approach gives the best of both: long-read contiguity polished to short-read accuracy.
- Short read — variant calling, large cohorts, lowest cost
- Long read — assembly, structural variants, plasmids
- Hybrid — complete, polished reference-grade genomes
We help teams pick the lightest strategy that still answers their question, then deliver an assembly with full QC metrics.