COV2HTML statistics

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Citations per year

Number of citations per year for the bioinformatics software tool COV2HTML

Tool usage distribution map

This map represents all the scientific publications referring to COV2HTML per scientific context
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Associated diseases

This word cloud represents COV2HTML usage per disease context

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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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