CAMP: A modular metagenomics analysis system for integrated multi-step data exploration.

Motivation: Computational analysis of large-scale metagenomics sequencing datasets have proven to be both incredibly valuable for extracting isolate-level taxonomic, and functional insights from complex microbial communities. However, due to an ever-expanding ecosystem of metagenomics-specific methods and file-formats, designing studies which implement seamless and scalable end-to-end workflows, and exploring the massive amounts of output data have become studies unto themselves. One-click bioinformatics pipelines have helped to organize these tools into targeted workflows, but they suffer from general compatibility and maintainability issues.

Computational Tools for the Analysis of Uncultivated Phage Genomes.

Over a century of bacteriophage research has uncovered a plethora of fundamental aspects of their biology, ecology, and evolution. Furthermore, the introduction of community-level studies through metagenomics has revealed unprecedented insights on the impact that phages have on a range of ecological and physiological processes. It was not until the introduction of viral metagenomics that we began to grasp the astonishing breadth of genetic diversity encompassed by phage genomes.

Accurate, Efficient and User-Friendly Mutation Calling and Sample Identification for TILLING Experiments.

TILLING (Targeting Induced Local Lesions IN Genomes) is a powerful reverse genetics method in plant functional genomics and breeding to identify mutagenized individuals with improved behavior for a trait of interest. Pooled high throughput sequencing (HTS) of the targeted genes allows efficient identification and sample assignment of variants within genes of interest in hundreds of individuals. Although TILLING has been used successfully in different crops and even applied to natural populations, one of the main issues for a successful TILLING experiment is that most currently available bioinformatics tools for variant detection are not designed to identify mutations with low frequencies in pooled samples or to perform sample identification from variants identified in overlapping pools.