Method for Sequencing a Polynucelotide Template

A method for sequencing nucleic acids, comprising

• (a) attaching a plurality of different nucleic acids to a surface;
• (b) amplifying the different nucleic acids on the surface to form a plurality of clusters on the surface, wherein clusters in the plurality of clusters abut or overlap with each other on the surface, wherein each of the clusters comprises copies of a single nucleic acid from the plurality of different nucleic acids;
• and
• (c) determining the sequences of the amplified copies in the clusters, wherein the sequences are determined by a method comprising:
• (i) obtaining images of overlapping signals emanating from the clusters that abut or overlap with each other on the surface, and
• (ii) processing the images to assign nucleic acid sequence information to a single cluster, wherein one or more nucleic acids in a cluster are distinguished from surrounding nucleic acids in the same cluster.

An automated system comprising instructions for

• a) attaching a plurality of different nucleic acids to a surface;
• (b) amplifying the different nucleic acids on the surface to form a plurality of clusters on the surface, wherein clusters in the plurality of clusters abut or overlap with each other on the surface, wherein each of the clusters comprises copies of a single nucleic acid from the plurality of different nucleic acids;
• and
• (c) determining the sequences of the amplified copies in the clusters, wherein the sequences are determined by a method comprising
• (i) obtaining images of overlapping signals emanating from the clusters that abut or overlap with each other on the surface, and
• (ii) processing the image to assign nucleic acid sequence information to a single cluster, wherein one or more nucleic acids in a cluster are distinguished from surrounding nucleic acids in the same cluster