BackgroundMetagenomics is limited in its ability to link distinct microbial populations to genetic potential due to a current lack of representative isolate genome sequences. Reference-independent approaches, which exploit for example inherent genomic signatures for the clustering of metagenomic fragments (binning), offer the prospect to resolve and reconstruct population-level genomic complements without the need for prior knowledge.ResultsWe present VizBin, a Java™-based application which offers efficient and intuitive reference-independent visualization of metagenomic datasets from single samples for subsequent human-in-the-loop inspection and binning. The method is based on nonlinear dimension reduction of genomic signatures and exploits the superior pattern recognition capabilities of the human eye-brain system for cluster identification and delineation. We demonstrate the general applicability of VizBin for the analysis of metagenomic sequence data by presenting results from two cellulolytic microbial communities and one human-borne microbial consortium. The superior performance of our application compared to other analogous metagenomic visualization and binning methods is also presented.ConclusionsVizBin can be applied de novo for the visualization and subsequent binning of metagenomic datasets from single samples, and it can be used for the post hoc inspection and refinement of automatically generated bins. Due to its computational efficiency, it can be run on common desktop machines and enables the analysis of complex metagenomic datasets in a matter of minutes. The software implementation is available at https://claczny.github.io/VizBin under the BSD License (four-clause) and runs under Microsoft Windows™, Apple Mac OS X™ (10.7 to 10.10), and Linux.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-014-0066-1) contains supplementary material, which is available to authorized users.

This note describes an information theory problem that arose from some analysis of quantum key distribution protocols. The problem seems very natural and is very easy to state but has not to our knowledge been addressed before in the information theory literature: suppose that we have a random bit string y of length n and we reveal k bits at random positions, preserving the order but without revealing the positions, how much information about y is revealed? We show that while the cardinality of the set of compatible y strings depends only on n and k, the amount of leakage does depend on the exact revealed x string. We observe that the maximal leakage, measured as decrease in the Shannon entropy of the space of possible bit strings, corresponds to the x string being all zeros or all ones and that the minimum leakage corresponds to the alternating x strings. We derive a formula for the maximum leakage (minimal entropy) in terms of n and k. We discuss the relevance of other measures of information, in particular min-entropy, in a cryptographic context. Finally, we describe a simulation tool to explore these results.

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We present an approach for performing the tallying work in the coercion-resistant JCJ voting protocol, introduced by Juels, Catalano, and Jakobsson, in linear time using fully homomorphic encryption (FHE). The suggested enhancement also paves the path towards making JCJ quantum-resistant, while leaving the underlying structure of JCJ intact. The pairwise comparison-based approach of JCJ using plaintext equivalence tests leads to a quadratic blow-up in the number of votes, which makes the tallying process rather impractical in realistic settings with a large number of voters. We show how the removal of invalid votes can be done in linear time via a solution based on recent advances in various FHE primitives such as hashing, zero-knowledge proofs of correct decryption, verifiable shuffles and threshold FHE. We conclude by touching upon some of the advantages and challenges of such an approach, followed by a discussion of further security and post-quantum considerations.

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