CodonCode Aligner is an easy-to-learn, easy-to-use program for sequence assembly, contig editing, and mutation detection. Aligner provides support for base calling, quality-based end clipping, vector trimming, sequence assembly and alignments, and fast navigation with user-definable criteria. CodonCode Aligner is available for Mac OS X and Microsoft Windows. Free demo and time-limited trial versions are available at www.codoncode.com/aligner/.

The genome assemblers generally take a file of short sequence reads and a file of quality-value as the input. Since the quality-value file for the high throughput short reads is usually highly memory-intensive, only a few assemblers, best suited for your assembly. For the sake of computational memory saving and convenience of data inquiry, high-throughput short reads data is always initially formatted to specific data structure. Currently, existing data structure for this usage can be predominantly classified into two categories: string-based model and graph-based model.

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