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COV2HTML specifications


Unique identifier OMICS_01302
Interface Web user interface
Restrictions to use None
Programming languages PHP, Python
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes




  • person_outline Marc Monot

Publication for COV2HTML

COV2HTML citations


Comparative transcriptomics analyses reveal the conservation of an ancestral infectious strategy in two bacteriophage genera

PMCID: 5563952
PMID: 28498372
DOI: 10.1038/ismej.2017.63
call_split See protocol

[…] lations, or phage to phage, before testing for differential expression.RNA-seq data have been deposited in NCBI-GEO with accession no. GSE86022.RNA-seq coverage visualization is available through the COV2HTML software at for a comparison of the host (0 min/13 min) and for a comparison of […]


The Mycobacterium tuberculosis transcriptional landscape under genotoxic stress

BMC Genomics
PMCID: 5057432
PMID: 27724857
DOI: 10.1186/s12864-016-3132-1
call_split See protocol

[…] Putative ncRNAs were identified with Rockhopper [, ] using default parameters for strand-specific reads, and then manually verified after visualization using Rockhopper viewer and COV2HTML []. In addition, a python script written using the two libraries matplotlib [] and seaborn [] to analyse and plot the coverage rate using different sizes of sliding windows across the reads a […]


What's a SNP between friends: The influence of single nucleotide polymorphisms on virulence and phenotypes of Clostridium difficile strain 630 and derivatives

PMCID: 5626343
PMID: 27652799
DOI: 10.1080/21505594.2016.1237333

[…] 5.The RNA-seq data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus database under the accession no. GSE72006RNA-seq coverage visualization is available through the COV2HTML software: […]


Next Generation “ omics” Approaches Reveal a Massive Alteration of Host RNA Metabolism during Bacteriophage Infection of Pseudomonas aeruginosa

PLoS Genet
PMCID: 4933390
PMID: 27380413
DOI: 10.1371/journal.pgen.1006134

[…] Unique Gene Reads that map to phage or host gene features respectively.RNA-Seq data have been deposited in NCBI-GEO with accession no. GSE76513.RNA-Seq coverage visualization is available through the COV2HTML software at [] for a comparison of the host (0 min / 13 min) and [] for a compari […]


Function of the CRISPR Cas System of the Human Pathogen Clostridium difficile

PMCID: 4556805
PMID: 26330515
DOI: 10.1128/mBio.01112-15
call_split See protocol

[…] 536, LN681537, LN681538, LN681539, LN681540, LN681541, LN681542, and PRJEB7856, respectively. RNA-seq coverage visualizations of the CRISPR loci are available for strain 630 through and for strain R20291 through (). […]


Expanding the RpoS/σS Network by RNA Sequencing and Identification of σS Controlled Small RNAs in Salmonella

PLoS One
PMCID: 4014581
PMID: 24810289
DOI: 10.1371/journal.pone.0096918

[…] nificance thresholds (0.05 and 0.001) were applied on adjusted p-values in order to declare genes as differentially expressed. The mapped reads were formatted into graph files for visualization using COV2HTML ( and GBrowse ( […]


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COV2HTML institution(s)
Laboratoire Pathogenese des Bacteries Anaerobies, Institut Pasteur, Paris, France; Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, Paris, France
COV2HTML funding source(s)
Supported by Institut Pasteur and Grant ERA-PTG/SAU/0002/2008 (ERA-NET PathoGenoMics).

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