ReadXplorer 2 - detailed read mapping analysis and visualization from one single source

Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A (2016)
Bioinformatics 32(24): 3702-3708.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
OA 514.54 KB
Hilker, Rolf; Stadermann, Kai BerndUniBi ; Schwengers, Oliver; Anisiforov, Evgeny; Jaenicke, Sebastian; Weisshaar, BerndUniBi ; Zimmermann, Tobias; Goesmann, Alexander
Abstract / Bemerkung
Motivation: The vast amount of already available and currently generated read mapping data re-quires comprehensive visualization, and should benefit from bioinformatics tools offering a wide spec-trum of analysis functionality from just one source. Appropriate handling of multiple mapped reads during mapping analyses remains an issue that demands improvement. Results: The capabilities of the read mapping analysis and visualization tool ReadXplorer were vastly enhanced. Here, we present an even finer granulated read mapping classification, improving the level of detail for analyses and visualizations. The spectrum of automatic analysis functions has been broadened to include genome rearrangement detection as well as correlation analysis between two mapping data sets. Existing functions were refined and enhanced, namely the computation of differ-entially expressed genes, the read count and normalization analysis and the transcription start site (TSS) detection. Additionally, ReadXplorer 2 features a highly improved support for large eukaryotic data sets and a command line version, enabling its integration into workflows. Finally, the new version is now able to display any kind of tabular results from other bioinformatics tools. Availability:
Page URI


Hilker R, Stadermann KB, Schwengers O, et al. ReadXplorer 2 - detailed read mapping analysis and visualization from one single source. Bioinformatics. 2016;32(24):3702-3708.
Hilker, R., Stadermann, K. B., Schwengers, O., Anisiforov, E., Jaenicke, S., Weisshaar, B., Zimmermann, T., et al. (2016). ReadXplorer 2 - detailed read mapping analysis and visualization from one single source. Bioinformatics, 32(24), 3702-3708. doi:10.1093/bioinformatics/btw541
Hilker, Rolf, Stadermann, Kai Bernd, Schwengers, Oliver, Anisiforov, Evgeny, Jaenicke, Sebastian, Weisshaar, Bernd, Zimmermann, Tobias, and Goesmann, Alexander. 2016. “ReadXplorer 2 - detailed read mapping analysis and visualization from one single source”. Bioinformatics 32 (24): 3702-3708.
Hilker, R., Stadermann, K. B., Schwengers, O., Anisiforov, E., Jaenicke, S., Weisshaar, B., Zimmermann, T., and Goesmann, A. (2016). ReadXplorer 2 - detailed read mapping analysis and visualization from one single source. Bioinformatics 32, 3702-3708.
Hilker, R., et al., 2016. ReadXplorer 2 - detailed read mapping analysis and visualization from one single source. Bioinformatics, 32(24), p 3702-3708.
R. Hilker, et al., “ReadXplorer 2 - detailed read mapping analysis and visualization from one single source”, Bioinformatics, vol. 32, 2016, pp. 3702-3708.
Hilker, R., Stadermann, K.B., Schwengers, O., Anisiforov, E., Jaenicke, S., Weisshaar, B., Zimmermann, T., Goesmann, A.: ReadXplorer 2 - detailed read mapping analysis and visualization from one single source. Bioinformatics. 32, 3702-3708 (2016).
Hilker, Rolf, Stadermann, Kai Bernd, Schwengers, Oliver, Anisiforov, Evgeny, Jaenicke, Sebastian, Weisshaar, Bernd, Zimmermann, Tobias, and Goesmann, Alexander. “ReadXplorer 2 - detailed read mapping analysis and visualization from one single source”. Bioinformatics 32.24 (2016): 3702-3708.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
Dieses Objekt ist durch das Urheberrecht und/oder verwandte Schutzrechte geschützt. [...]
Access Level
OA Open Access
Zuletzt Hochgeladen
MD5 Prüfsumme

19 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Identifying the Growth Modulon of Corynebacterium glutamicum.
Haas T, Graf M, Nieß A, Busche T, Kalinowski J, Blombach B, Takors R., Front Microbiol 10(), 2019
PMID: 31134020
A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani.
Verwaaijen B, Wibberg D, Winkler A, Zrenner R, Bednarz H, Niehaus K, Grosch R, Pühler A, Schlüter A., Sci Rep 9(1), 2019
PMID: 31076623
Salmonella Establishment in Agricultural Soil and Colonization of Crop Plants Depend on Soil Type and Plant Species.
Jechalke S, Schierstaedt J, Becker M, Flemer B, Grosch R, Smalla K, Schikora A., Front Microbiol 10(), 2019
PMID: 31156568
The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16.
Arenas-López C, Locker J, Orol D, Walter F, Busche T, Kalinowski J, Minton NP, Kovács K, Winzer K., Biotechnol Biofuels 12(), 2019
PMID: 31236137
Overlap of Promoter Recognition Specificity of Stress Response Sigma Factors SigD and SigH in Corynebacterium glutamicum ATCC 13032.
Dostálová H, Busche T, Holátko J, Rucká L, Štěpánek V, Barvík I, Nešvera J, Kalinowski J, Pátek M., Front Microbiol 9(), 2018
PMID: 30687273
On the Enigma of Glutathione-Dependent Styrene Degradation in Gordonia rubripertincta CWB2.
Heine T, Zimmerling J, Ballmann A, Kleeberg SB, Rückert C, Busche T, Winkler A, Kalinowski J, Poetsch A, Scholtissek A, Oelschlägel M, Schmidt G, Tischler D., Appl Environ Microbiol 84(9), 2018
PMID: 29475871
Three previously unrecognised classes of biosynthetic enzymes revealed during the production of xenovulene A.
Schor R, Schotte C, Wibberg D, Kalinowski J, Cox RJ., Nat Commun 9(1), 2018
PMID: 29773797
Multi-Omics and Targeted Approaches to Determine the Role of Cellular Proteases in Streptomyces Protein Secretion.
Busche T, Tsolis KC, Koepff J, Rebets Y, Rückert C, Hamed MB, Bleidt A, Wiechert W, Lopatniuk M, Yousra A, Anné J, Karamanou S, Oldiges M, Kalinowski J, Luzhetskyy A, Economou A., Front Microbiol 9(), 2018
PMID: 29915569
Deciphering the Adaptation of Corynebacterium glutamicum in Transition from Aerobiosis via Microaerobiosis to Anaerobiosis.
Lange J, Münch E, Müller J, Busche T, Kalinowski J, Takors R, Blombach B., Genes (Basel) 9(6), 2018
PMID: 29899275
Binning enables efficient host genome reconstruction in cnidarian holobionts.
Celis JS, Wibberg D, Ramírez-Portilla C, Rupp O, Sczyrba A, Winkler A, Kalinowski J, Wilke T., Gigascience 7(7), 2018
PMID: 29917104
BAC-BROWSER: The Tool for Visualization and Analysis of Prokaryotic Genomes.
Garanina IA, Fisunov GY, Govorun VM., Front Microbiol 9(), 2018
PMID: 30519231
Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions.
Rebets Y, Tsolis KC, Guðmundsdóttir EE, Koepff J, Wawiernia B, Busche T, Bleidt A, Horbal L, Myronovskyi M, Ahmed Y, Wiechert W, Rückert C, Hamed MB, Bilyk B, Anné J, Friðjónsson Ó, Kalinowski J, Oldiges M, Economou A, Luzhetskyy A., Front Microbiol 9(), 2018
PMID: 30619125
The AGXX® Antimicrobial Coating Causes a Thiol-Specific Oxidative Stress Response and Protein S-bacillithiolation in Staphylococcus aureus.
Loi VV, Busche T, Preuß T, Kalinowski J, Bernhardt J, Antelmann H., Front Microbiol 9(), 2018
PMID: 30619128
The Rhizoctonia solani AG1-IB (isolate 7/3/14) transcriptome during interaction with the host plant lettuce (Lactuca sativa L.).
Verwaaijen B, Wibberg D, Kröber M, Winkler A, Zrenner R, Bednarz H, Niehaus K, Grosch R, Pühler A, Schlüter A., PLoS One 12(5), 2017
PMID: 28486484
Refined annotation of the complete genome of the phytopathogenic and xanthan producing Xanthomonas campestris pv. campestris strain B100 based on RNA sequence data.
Alkhateeb RS, Rückert C, Rupp O, Pucker B, Hublik G, Wibberg D, Niehaus K, Pühler A, Vorhölter FJ., J Biotechnol 253(), 2017
PMID: 28506932
Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes.
Capistrano-Gossmann GG, Ries D, Holtgräwe D, Minoche A, Kraft T, Frerichmann SLM, Rosleff Soerensen T, Dohm JC, González I, Schilhabel M, Varrelmann M, Tschoep H, Uphoff H, Schütze K, Borchardt D, Toerjek O, Mechelke W, Lein JC, Schechert AW, Frese L, Himmelbauer H, Weisshaar B, Kopisch-Obuch FJ., Nat Commun 8(), 2017
PMID: 28585529
Physiological roles of sigma factor SigD in Corynebacterium glutamicum.
Taniguchi H, Busche T, Patschkowski T, Niehaus K, Pátek M, Kalinowski J, Wendisch VF., BMC Microbiol 17(1), 2017
PMID: 28701150
Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris.
Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ., Microbiology 163(8), 2017
PMID: 28795660
The transcriptional regulator LysG (Rv1985c) of Mycobacterium tuberculosis activates lysE (Rv1986) in a lysine-dependent manner.
Schneefeld M, Busche T, Geffers R, Kalinowski J, Bange FC., PLoS One 12(10), 2017
PMID: 29049397

32 References

Daten bereitgestellt von Europe PubMed Central.

HTSeq--a Python framework to work with high-throughput sequencing data.
Anders S, Pyl PT, Huber W., Bioinformatics 31(2), 2014
PMID: 25260700
High-throughput sequencing technologies.
Reuter JA, Spacek DV, Snyder MP., Mol. Cell 58(4), 2015
PMID: 26000844
Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique.
Pfeifer-Sancar K, Mentz A, Ruckert C, Kalinowski J., BMC Genomics 14(), 2013
PMID: 24341750
Savant Genome Browser 2: visualization and analysis for population-scale genomics.
Fiume M, Smith EJ, Brook A, Strbenac D, Turner B, Mezlini AM, Robinson MD, Wodak SJ, Brudno M., Nucleic Acids Res. 40(Web Server issue), 2012
PMID: 22638571
GenomeView: a next-generation genome browser.
Abeel T, Van Parys T, Saeys Y, Galagan J, Van de Peer Y., Nucleic Acids Res. 40(2), 2011
PMID: 22102585
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B., Nat. Methods 5(7), 2008
PMID: 18516045
Differential expression analysis for sequence count data.
Anders S, Huber W., Genome Biol. 11(10), 2010
PMID: 20979621
Repetitive DNA and next-generation sequencing: computational challenges and solutions.
Treangen TJ, Salzberg SL., Nat. Rev. Genet. 13(1), 2011
PMID: 22124482
TSSAR: TSS annotation regime for dRNA-seq data.
Amman F, Wolfinger MT, Lorenz R, Hofacker IL, Stadler PF, Findeiß S., BMC Bioinformatics 15(), 2014
PMID: 24674136
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.
Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK., Genome Res. 22(3), 2012
PMID: 22300766
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L., Nat. Biotechnol. 28(5), 2010
PMID: 20436464
Computational analysis of bacterial RNA-Seq data.
McClure R, Balasubramanian D, Sun Y, Bobrovskyy M, Sumby P, Genco CA, Vanderpool CK, Tjaden B., Nucleic Acids Res. 41(14), 2013
PMID: 23716638
Interclonal gradient of virulence in the Pseudomonas aeruginosa pangenome from disease and environment.
Hilker R, Munder A, Klockgether J, Losada PM, Chouvarine P, Cramer N, Davenport CF, Dethlefsen S, Fischer S, Peng H, Schonfelder T, Turk O, Wiehlmann L, Wolbeling F, Gulbins E, Goesmann A, Tummler B., Environ. Microbiol. 17(1), 2014
PMID: 25156090
RNA-Seq gene expression estimation with read mapping uncertainty.
Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN., Bioinformatics 26(4), 2009
PMID: 20022975
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.
Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE., Bioinformatics 25(20), 2009
PMID: 19654113
Detection of large-scale variation in the human genome.
Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C., Nat. Genet. 36(9), 2004
PMID: 15286789
Integrative genomics viewer.
Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP., Nat. Biotechnol. 29(1), 2011
PMID: 21221095
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.
Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, Legoix-ne P, Nicolas A, Delattre O, Barillot E., Bioinformatics 26(15), 2010
PMID: 20639544
Emerging technologies for the clinical microbiology laboratory.
Buchan BW, Ledeboer NA., Clin. Microbiol. Rev. 27(4), 2014
PMID: 25278575
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.
Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA., Bioinformatics 28(4), 2011
PMID: 22199388
Genome sequencing in microfabricated high-density picolitre reactors.
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM., Nature 437(7057), 2005
PMID: 16056220
Accurate whole human genome sequencing using reversible terminator chemistry.
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ., Nature 456(7218), 2008
PMID: 18987734
ReadXplorer--visualization and analysis of mapped sequences.
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A., Bioinformatics 30(16), 2014
PMID: 24790157
High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates.
Dugar G, Herbig A, Forstner KU, Heidrich N, Reinhardt R, Nieselt K, Sharma CM., PLoS Genet. 9(5), 2013
PMID: 23696746
A geometric approach for classification and comparison of structural variants.
Sindi S, Helman E, Bashir A, Raphael BJ., Bioinformatics 25(12), 2009
PMID: 19477992
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Love MI, Huber W, Anders S., Genome Biol. 15(12), 2014
PMID: 25516281

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

PMID: 27540267
PubMed | Europe PMC

Suchen in

Google Scholar