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Phage Term Virome (version 2.0.0)

Single or Paired-end reads:

Select between paired and single end data

Select first set of reads:

Specify dataset with forward reads

Select second set of reads:

Specify dataset with reverse reads

Phage reads (FASTQ):

Phage sequencing reads file in fastq format from randomly fragmented NGS data (e.g. Illumina TruSeq) but NOT Nextera.

Phage genome (FASTA):

Phage reference genome file in fasta format, Multi-fasta NOT accepted.

Output files prefix:

Prefix for the output file name.

Bacterial host genome (FASTA):

Host reference genome file in fasta format, Multi-fasta NOT accepted. Warning : increases process time.

Seed length:

Seed length value for alignment of reads.

Peak surrounding region:

Length of the surrounding region defining close peaks to be merged in the analysis process.

Limit coverage:

Phage upper limit coverage.

Limit phage lenght:

Minimum phage fasta length.

What it does

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).

Inputs

Raw reads file(s) in fastq format : paired-ends or single-ends.

Phage genome in fasta format

Host genome in fasta format (optional)

Outputs

PDF report

Statistical table (csv)

FASTA file(s) re-organized to start at the predicted termini

Tool version

Version: 4.0.0 Commit SHA: 5e92822b3f289a329d18914b2183159642abdba4