PhageTerm pipeline

PhageTerm specifications


Unique identifier OMICS_16275
Name PhageTerm
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data The sequencing reads, the corresponding assembled phage genome.
Input format FASTQ, FASTA
Output data The mapped reads, the starting position coverage (SPC), the coverage (COV) in each orientation.
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.7
Stability Stable
Requirements Matplotlib, numpy, pandas, sklearn, scipy, statsmodels, reportlab
Maintained Yes



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  • person_outline Marc Monot <>

Publication for PhageTerm

PhageTerm IN pipeline

PMCID: 5923482
PMID: 29642590
DOI: 10.3390/v10040188

[…] , are genome ends resolved?, is genome supported by adequate even coverage?, reads that passed faqcs and the consensus sequence obtained from genome assembly were submitted for analysis using phageterm software. both phages contain direct terminal repeats (dtrs). pseudomonas phage vb_paep_130_113 contains a short 463 bp dtr and staphylococcus phage vb_saum_0414_108 has a long dtr spanning […]

PhageTerm funding source(s)
This work was supported by a discovery grant from the Natural Sciences and Engineering Research Council of Canada (NSERC #341450-2010), the Agence Nationale de la Recherche (“CloSTARn”, ANR-13-JSV3-0005-01) and the french Government's Investissement d'Avenir program; Laboratoire d'Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (ANR-10-LABX-62-IBEID).

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