Florence Computational Biology Group
Tools and software
Tn-Core
Tn-Core is a toolbox for integrating Tn-seq gene essentiality data and constraint-based metabolic modelling. Tn-Core is a MATLAB toolbox that contains several custom functions, and it is built upon existing functions within the COBRA Toolbox and the TIGER Toolbox. Tn-Core takes as input a genome-scale metabolic model, Tn-seq data, and optionally RNA-seq data, and returns: i) a context-specific core metabolic model; ii) an evaluation of redundancies within core metabolic pathways, and optionally iii) a refined genome-scale metabolic model. A simple, user-friendly workflow, requiring limited knowledge of metabolic modelling, is provided that allows users to run the analyses and export the data as easy-to-explore files of value to both experimental and computational biologists.
MeDuSa
Medusa is an algorithm for genome scaffolding. MEDUSA exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. In contrast to currently used scaffolders, it does not require either prior knowledge on the microrganisms dataset under analysis (e.g. their phylogenetic relationships) or the availability of paired end read libraries. This makes usability and running time two additional important features of our method. Moreover, benchmarks and tests on real bacterial datasets showed that MEDUSA is highly accurate and, in most cases, outperforms traditional scaffolders.
Webserver --- GitHub project download --- Article
CONTIGuator: A bacterial genomes finishing tool for structural insights on draft genomes.
A software tool for contigs mapping over a reference genome which allows the visualization of a map of contigs, underlining loss and/or gain of genetic elements and permitting to finish multipartite genomes
Project website --- Latest version download --- Get involved on GitHub! --- Article
StreamingTrim 1.0: a Java software for dynamic trimming of 16S rRNA sequence data from metagenetic studies.
StreamingTrim is a DNA reads trimming software able to analyse the quality of DNA sequences searching for low-quality zones in a very conservative way. This software has been developed with the aim to provide an easy-to-use tool capable of trimming second-generation sequencing data, retaining as much information as possible.
Enly: enlarge your contigs
Enly, a simple tool based on the iterative mapping of sequence reads at contig edges, capable to extend the genomic contigs deriving from high-throughput sequencing, especially those deriving by Newbler-like assemblies.
Ductape: A suite for the analysis and correlation of genomic and OmniLog™ Phenotype Microarray data
DuctApe is a software suite that will help bioinformaticians to analyze genomes AND phenomic experiments. The final purpose of the program is to combine the genomic informations (encoded as KEGG pathways) with the results of phenomic experiments (Phenotype Microarrays) and highlight the genes that may be responsible for phenotypic variations. DuctApe it's written in python and works as a command line tool for Unix environments.