Nucleic Acid Sequencing Algorithm Using Mutated Reads

The patent applies preliminary action by introducing mutations into target template nucleic acid molecules before sequencing. This pre-mutation step creates distinctive mutation patterns that serve as markers, enabling accurate assembly of short sequence reads even in repeat regions. The mutations are introduced in advance so that when sequence reads are assembled, the mutation patterns provide information about the original template structure, resolving ambiguities in repeat regions and structural variants.

The patent uses mutation patterns as an intermediary to bridge the gap between short sequence reads and accurate assembly. The introduced mutations act as mediators that carry information about the original template structure through the sequencing and assembly process. By analyzing these intermediary mutation patterns, the system can accurately reconstruct sequences even when direct assembly of short reads would be ambiguous.

The patent extracts and utilizes only the essential mutation pattern information needed for assembly, rather than processing all sequence data through complex consensus algorithms. By focusing specifically on the introduced mutations as markers, the method simplifies the assembly process while maintaining accuracy. The mutation patterns are extracted as key features that directly inform assembly decisions without requiring full consensus sequence creation.

The patent changes the approach from traditional consensus sequence creation to mutation pattern analysis. Instead of processing sequence data through complex consensus algorithms that compare all reads at each position, the method transforms the problem into analyzing predefined mutation patterns. This parameter change from sequence alignment to mutation pattern matching reduces computational complexity while preserving assembly accuracy.

The patent applies local quality by introducing specific mutations at particular locations in target template nucleic acid molecules. These localized mutations create distinctive mutation patterns that serve as unique identifiers for each template molecule. When multiple molecules are sequenced simultaneously, these local mutation markers enable differentiation between templates even in repeat regions, as each template carries its specific mutation signature at defined positions.

The patent uses preliminary action by pre-introducing mutations into target templates before pooling and sequencing multiple molecules together. This advance mutation step ensures that even when molecules are processed simultaneously, each retains its unique mutation pattern. The preliminary mutation introduces distinguishing features that persist through the multiplexed sequencing process, enabling accurate differentiation and assembly of sequences from multiple templates.