Compositions and methods for identification of a duplicate sequencing read
The present invention provides methods, compositions and kits for detecting duplicate sequencing reads. In some embodiments, the duplicate sequencing reads are removed.
1. A method for detecting duplicate sequencing reads, the method comprising:
ligating an adaptor to each of a plurality of nucleic acid fragments, wherein each adaptor comprises a unique identifier having from about 1 to about 8 nucleotides, an indexing site unique to a subset of the adaptors, and a primer binding site;
amplifying the adaptor-ligated fragments into amplicons;
sequencing the amplicons to produce sequence reads that include identifier and target sequences; and
identifying sequence reads with identical identifier and target sequences as duplicates.
2. The method of claim 1 , further comprising removing a duplicate read from the sequence reads.
3. The method of claim 1 , wherein the identifier site is sequenced with the target sequence.
4. The method of claim 1 , wherein the identifier site is sequenced separately from the target sequence.
5. The method of claim 1 , wherein the nucleic acid fragments comprise RNA.
6. The method of claim 1 , wherein the nucleic acid fragments are genomic DNA fragments or cDNA fragments.
7. The method of claim 1 , wherein the primer binding site is a universal target sequencing primer binding site.
8. The method of claim 1 , wherein each unique identifier is 6 nucleotides in length.
9. The method of claim 1 , wherein each unique identifier is 8 nucleotides in length.
10. The method of claim 1 , wherein each unique identifier is at a junction between the adapter and the nucleic fragment.