Sequence assembly
View Patent ↗The invention relates to assembly of sequence reads. The invention provides a method for identifying a mutation in a nucleic acid involving sequencing nucleic acid to generate a plurality of sequence reads. Reads are assembled to form a contig, which is aligned to a reference. Individual reads are aligned to the contig. Mutations are identified based on the alignments to the reference and to the contig.
1. A system for identifying a mutation in a nucleic acid, the system comprising:
a computing device including a tangible, non-transitory memory coupled to a processor configured to execute computer program instructions to cause the processor to:
receive a plurality of sequence reads;
create a contig based on the reads;
align the contig to a reference sequence;
align the individual reads back to the contig; and
identify a mutation based on the alignments to the contig and the reference sequence.
2. The system of claim 1 , wherein the computing device is further configured to divide the reads into subsets.
3. The system of claim 1 , wherein the computing device is further configured to determine a position of the mutation in the nucleic acid.
4. The system of claim 1 , wherein the mutation is selected from the group consisting of: a single nucleotide polymorphism (SNP), an insertion, a deletion, a substitution, a translocation, and a copy number variation.
5. The system of claim 1 , wherein the computing device is configured to identify a plurality of mutations.
6. The system of claim 5 , wherein a first mutation is within about 100 nucleotides of a second mutation.
7. The system according to claim 6 , wherein the first mutation is a substitution and the second mutation is a deletion.
8. The system of claim 1 wherein the mutation is a deletion at an end of a sequence read.
9. The system of claim 1 , wherein the mutation is associated with a disease.