COV2HTML protocols

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COV2HTML specifications

Information


Unique identifier OMICS_01302
Name COV2HTML
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

Subtool


  • MAP2COV

Maintainer


  • person_outline Marc Monot <>

Publication for COV2HTML

COV2HTML in pipelines

 (3)
2017
PMCID: 5563952
PMID: 28498372
DOI: 10.1038/ismej.2017.63

[…] 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 https://mmonot.eu/cov2html/visualisation.php?str_id=-36 for a comparison of the host (0 min/13 min) and https://mmonot.eu/cov2html/visualisation.php?str_id=-38 for a comparison […]

2013
PMCID: 3649979
PMID: 23675309
DOI: 10.1371/journal.pgen.1003493

[…] converted into bam files with the samtools script (). the data were visualized at a strand-specific manner (for 5′-end rna-seq libraries) or as a whole transcript coverage map (for rna-seq) using cov2html (marc monot, submitted). all tsss detected by 5′-end rna-seq were inspected manually to identify potential srnas. to estimate the relevance of each tss, a score was computed […]

2013
PMCID: 3789822
PMID: 24098137
DOI: 10.1371/journal.pgen.1003756

[…] after illumina sequencing, the reads were mapped to the c. difficile genome using bowtie then converted into bam files with the samtools . the data were visualized at a strand-specific manner using cov2html (http://mmonot.eu/cov2html/). all tss detected by rna-seq were inspected manually. deep sequencing data are available at https://mmonot.eu/cov2html/visualisation.php?str_id=-14., to perform […]


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COV2HTML in publications

 (6)
PMCID: 5057432
PMID: 27724857
DOI: 10.1186/s12864-016-3132-1

[…] in clusters., 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 […]

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

[…] mbp, 66.3% gc content and 6,267 predicted orfs). next, a detailed genome reannotation was performed based on rna-seq data generated from exponentially growing and uninfected pak cells ()., using cov2html [] to visualize transcripts, we manually reannotated 32 open reading frames (orfs) (by detection of an alternative start codon) and defined 63 new putative coding sequences. among them, 39 […]

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

[…] ln681537, ln681538, ln681539, ln681540, ln681541, ln681542, and prjeb7856, respectively. rna-seq coverage visualizations of the crispr loci are available for strain 630 through https://mmonot.eu/cov2html/visualisation.php?str_id=-17 and for strain r20291 through http://mmonot.eu/cov2html/visualisation.php?str_id=-18 ()., citation boudry p, semenova e, monot m, datsenko ka, lopatina a, […]

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

[…] 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 (https://mmonot.eu/cov2html) and gbrowse (http://genopole.pasteur.fr/gbrowse/)., the rna-seq data discussed in this publication have been deposited in ncbi’s gene expression omnibus […]

PMCID: 3789822
PMID: 24098137
DOI: 10.1371/journal.pgen.1003756

[…] after illumina sequencing, the reads were mapped to the c. difficile genome using bowtie then converted into bam files with the samtools . the data were visualized at a strand-specific manner using cov2html (http://mmonot.eu/cov2html/). all tss detected by rna-seq were inspected manually. deep sequencing data are available at https://mmonot.eu/cov2html/visualisation.php?str_id=-14., to perform […]


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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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