PhageTerm: a Fast and User-friendly Software to Determine Bacteriophage Termini and Packaging Mode using randomly fragmented NGS data

Bacteriophages produce viron particles protecting their nucleic acid content, mainly as linear dsDNA form. In this study we investigate how the information gathered by high throughput sequencing technologies can be used to determine the DNA termini and packaging mechanisms of dsDNA phages. The wet-lab procedures traditionally used for this purpose rely on the identification and cloning of restriction fragment which can be delicate and cumbersome. Here, we developed a theoretical and statistical framework to analyze DNA termini and phage packaging mechanisms using next-generation sequencing data. A software, PhageTerm, was validated on a set of phages with well-established packaging mechanisms representative of the termini diversity: 5′cos (lambda), 3′cos (Efm1), pac (P1), headful without a pac site (T4), DTR (T7) and host fragment (Mu). In addition, we applied our methods to decipher the termini of 9 Clostridium difficile phages and 5 phages whose sequences where retrieved from the sequence read archive (SRA). Our methods are implemented in the PhageTerm software which we are making freely available. For direct graphical interface operation, a Galaxy wrapper version is also available at https://galaxy.pasteur.fr.