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Image analysis and base-calling were performed using the Illumina Pipeline, where sequence tags were obtained after quality filtering.

In SAMtools, base-calling was performed using the "mpileup" command and the "-E -D -S -u" parameters of SAMtools 0.1.18.

Base-calling was performed using the Genome Analyzer Pipeline.

Base-calling was performed using Illumina's RTA version 1.12.4.2.

Base-calling was performed using the bundled 454 software.

Base-calling was performed using the Phred program.

Base-calling was performed using PHRED [ 66, 67] on chromatogram traces.

Cluster detection and base calling were performed using RTAv1.13 and quality of reads assessed with CASAVA v1.8.1 (Illumina).

Image analysis and base calling were performed using the HiSeq Control Software and RTA component from Illumina.

Image recognition and base calling were performed using the Illumina Pipeline.

Image analysis and base calling were performed using Illumina software.