| PhageTermVirome software is a tool to determine phage genome termini and genome packaging mode on single phage or multiple contigs at once. The software uses phage and virome sequencing reads obtained from libraries prepared with DNA fragmented randomly (e.g. Covaris fragmentation, and library preparation using Illumina TruSeq). Phage or virome sequencing reads (fastq files) are aligned to the assembled phage genome or assembled virome (fasta or multifasta files) in order to calculate two types of coverage values (whole genome coverage and the Starting Position Coverage (SPC)). The starting position coverage is used to perform a detailed termini and packaging mode analysis. Mu-type phage analysis : can be done if user suspect the phage genome to be Mu-like type (Only for single phage genome analysis, not possible with multifasta file) : User can also provide the host (bacterial) genome sequence. The Mu-type phage analysis will take the reads that does not match the phage genome and align them on the bacterial genome using the same mapping function. The analysis to identify Mu-like phages is available only when providing a single phage genome (not possible if user provide a multi-fast file with multiple assembled phage contigs). |
hg clone https://toolshed.g2.bx.psu.edu/repos/bioit_sciensano/phagetermvirome
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Determine phage genome termini and genome packaging mode on single phage or multiple contigs at once. | 2.0.0 | 19.05 | |