The major difference between Sanger sequencing and NGS is the sequencing volume.

Sanger sequencing only sequences one DNA fragment at a time. On the other hand, NGS is massively parallel, sequencing millions of fragments simultaneously. NGS also offers greater discovery power for the detection of novel or rare variants.

Sanger sequencing is the preferred technique for:

• Sequencing single genes
• Sequencing up to 96 samples at a time without barcoding
• Microbial identification
• Sequencing 1-100 amplicon targets at the lowest cost
• Microsatellite or STR analysis
• Fragment analysis
• NGS confirmation

NGS is the preferred technique for:

• Cost-effective sequencing of hundreds to thousands of gene or gene regions simultaneously
• Faster turnaround times for high sample volumes
• Sequencing samples with low input amounts of starting material
• Comprehensive genome coverage
• Identifying novel, low-frequency variants by expanding the number of targets sequenced in a single run