MEDUSA (Multi-Draft based Scaffolder)
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.
BLAST2Network: A tool for the analysis of chromosome and plasmid genes by phylogenetic profiling and the visualization of their similarity relationships.
CONTIGuator: A bacterial genomes finishing tool for structural insights on draft genomes.
CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome finishing process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT)
DuctApe - a tool for the analysis and correlation of genomic and high throughput phenotypic Biolog data (Accepted in "Genomics")
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.