COV2HTML: a visualization and analysis tool of bacterial next generation sequencing (NGS) data for postgenomics life scientists.

COV2HTML is an interactive web interface, which is addressed to biologists, and allows performing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). It combines two processes: a tool that converts the huge NGS mapping or coverage files into light specific coverage files containing information on genetic elements; and a visualization interface allowing a real-time analysis of data with optional integration of statistical results. To demonstrate the scope of COV2HTML, the program was tested with data from two published studies. The first data were from RNA-seq analysis of Campylobacter jejuni, based on comparison of two conditions with two replicates. We were able to recover 26 out of 27 genes highlighted in the publication using COV2HTML. The second data comprised of stranded TSS and RNA-seq data sets on the Archaea Sulfolobus solfataricus. COV2HTML was able to highlight most of the TSSs from the article and allows biologists to visualize both TSS and RNA-seq on the same screen. The strength of the COV2HTML interface is making possible NGS data analysis without software installation, login, or a long training period. A web version is accessible at https://mmonot.eu/COV2HTML/ . This website is free and open to users without any login requirement.

[1]  E M Rubin,et al.  Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing , 2009, Proceedings of the National Academy of Sciences.

[2]  Bronwyn G. Butcher,et al.  Characterization of the Fur Regulon in Pseudomonas syringae pv. tomato DC3000 , 2011, Journal of bacteriology.

[3]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[4]  J. Rougemont,et al.  Comparative genomic and phylogeographic analysis of Mycobacterium leprae , 2009, Nature Genetics.

[5]  Allen D. Delaney,et al.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing , 2007, Nature Methods.

[6]  Nicholas M. Luscombe,et al.  Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli , 2010, Nucleic acids research.

[7]  M. Ohnishi,et al.  Complete Sequencing of the bla NDM-1-Positive IncA/C Plasmid from Escherichia coli ST38 Isolate Suggests a Possible Origin from Plant Pathogens , 2011, PloS one.

[8]  D. Maskell,et al.  Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome , 2011, Microbiology.

[9]  Samuel A. Assefa,et al.  A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi , 2009, PLoS genetics.

[10]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[11]  Zhoutao Chen,et al.  Ribosomal RNA depletion for massively parallel bacterial RNA-sequencing applications. , 2011, Methods in molecular biology.

[12]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[13]  Dan Wu,et al.  EMBL Nucleotide Sequence Database in 2006 , 2006, Nucleic Acids Res..

[14]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[15]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[16]  Matthew Berriman,et al.  BamView: visualizing and interpretation of next-generation sequencing read alignments , 2012, Briefings Bioinform..

[17]  Pimlapas Leekitcharoenphon,et al.  The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium , 2012, Proceedings of the National Academy of Sciences.

[18]  Hanlee P. Ji,et al.  Next-generation DNA sequencing , 2008, Nature Biotechnology.

[19]  Brian D. Ondov,et al.  Structure and Complexity of a Bacterial Transcriptome , 2009, Journal of bacteriology.

[20]  B. Simmons,et al.  A single-base resolution map of an archaeal transcriptome. , 2010, Genome research.

[21]  J. Galagan,et al.  A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data , 2009, Genome Biology.

[22]  Sandrine Dudoit,et al.  Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments , 2010, BMC Bioinformatics.

[23]  L. Stein,et al.  JBrowse: a next-generation genome browser. , 2009, Genome research.

[24]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[25]  W. Michalski,et al.  Resequencing the Mycobacterium avium subsp. paratuberculosis K10 Genome: Improved Annotation and Revised Genome Sequence , 2010, Journal of bacteriology.