Additional File 2.

Reduction of the number of clusters identified in tile images due to identical tag sequences. If all or the vast majority sequences start identical in the first read of a sequencing run, image analysis will consider a higher fraction of the clusters as being grown into each other and remove them. This effect is for example observed if libraries are made from restriction digested molecules or if tag/barcode sequences are added on the outer molecule edges and read in the first read. Changing parameters for an image offline analysis (Firecrest module) can be used as a work-a-round. The figure table shows cluster counts as well as a section of the image of the same tile in cycle 1 and 4 for a run from the Neandertal Genome project (Green et al: Science 2010) 080902_BIOLAB29_Run_PE51_1 in which the tag 'GAC' was read in the beginning of the first read. Cluster counts were obtained from IPAR v1.01 image analysis (cluster identification based only on the first cycle of the run) and the results for a version of the Firecrest v1.9.5 algorithm, in which cluster identification was done in cycle 4.

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Kircher et al. BMC Genomics 2011 12:382   doi:10.1186/1471-2164-12-382