PhageTerm protocols

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PhageTerm specifications

Information


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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Maintainer


  • person_outline Marc Monot <>

Publication for PhageTerm

PhageTerm in pipeline

2018
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 […]


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PhageTerm in publications

 (4)
PMCID: 5923482
PMID: 29642590
DOI: 10.3390/v10040188

[…] expected value (virus family being determined either by morphological characteristics, closest sequenced relatives, or both)., the genomic termini and phage packaging strategy were determined using phageterm []. briefly, faqcs processed reads were aligned to the putative phage genome and read build-ups, indicative of over-represented fragment ends, were identified. phageterm uses the starting […]

PMCID: 5883640
PMID: 29615108
DOI: 10.1186/s40168-018-0452-1

[…] lagaffe is also flanked by direct repeats, whereas a sequence composed of inverted repeats is expected to form the integration site of is30 transposases []. analysis of lagaffe reads with the phageterm tool [], dedicated to the detection of the strategy used by phages to package their genome into capsids, identified the cos region of lagaffe, upstream of the terminase gene terms.fig. 3, […]

PMCID: 5869516
PMID: 29534436
DOI: 10.3390/v10030123

[…] by keeping the naïve hosts that are immune to infection for a while, and then return to being sensitive to infection, providing new “grass” for the phage to prey on., marc monot then described the phageterm tool, which allows a fast and accurate determination of the packaging mechanism (cos versus headful). this tool brilliantly exploits new generation sequencing (ngs) read number biases […]

PMCID: 5511896
PMID: 28705957
DOI: 10.1128/genomeA.00333-17

[…] the 17,814 raw reads (total of 6,821,949 bases) were assembled into one contig using the gs de novo assembler (roche), with an average coverage of 122-fold. genomic termini were determined using phageterm (). phage ms1 has a circularly permuted genome and uses headful (pac-type) packaging system. the genome of the virulent pneumococcal phage ms1 has a low g+c content (42.3%), and is composed […]


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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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