Circonspect Tool for creating contig spectra
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Circonspect Description

Circonspect, also known as, Control In Research on CONtig SPECTra) was created in order to generate contig spectra that is based on the assembly of random subsets of metagenomes. The contig spectra can then be modeled downstream to get diversity estimates (for example with PHACCS). Different kind of contig spectra can be created: the standard contig spectrum for alpha-diversity, the mixed contig spectrum, for gamma-diversity, and the cross-contig spectrum, for beta diversity. Building a cross-contig spectrum requires building a mixed contig spectrum, which requires building normal contig spectra based on several selected metagenomes (FASTA files). Circonspect uses a indexed sequence database to store temporary data. Any assembly program that support a minimum overlap length and similarity is adapted; at this time, Minimo, TIGR Assembler, LIGR Assembler, CAP3 and Newbler are supported. When multiple repetitions are done (bootstrapping), the average contig spectrum is calculated. The user can control the size of the sequences by trimming them to a given length and removing sequences smaller than a threshold.

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