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BamView: visualizing and interpretation of next-generation sequencing read alignments

T. Carver, S. R. Harris, T. D. Otto, M. Berriman, J. Parkhill, J. A. McQuillan
2012 Briefings in Bioinformatics  
BamView has been developed to visualize and analyse sequence reads from NGS platforms, which have been aligned to a reference sequence.  ...  It is a desktop application for browsing the aligned or mapped reads [Ruffalo, M, LaFramboise, T, Koyutu« rk, M. Comparative analysis of algorithms for next-generation sequencing read alignment.  ...  FUTURE DIRECTIONS BamView within Artemis and ACT provides a powerful tool for visualizing, interpreting and analysing next generation sequence data sets.  ... 
doi:10.1093/bib/bbr073 pmid:22253280 pmcid:PMC3603209 fatcat:kro24phha5hthoyopfyddnpd6i

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

T. Carver, S. R. Harris, M. Berriman, J. Parkhill, J. A. McQuillan
2011 Bioinformatics  
Results: We present Artemis as a tool for integrated visualization and computational analysis of different types of HTS datasets in the context of a reference genome and its corresponding annotation.  ...  An explosion in the type, not just number, of sequencing experiments has also taken place including genome re-sequencing, population-scale variation detection, whole transcriptome sequencing and genome-wide  ...  BamView was originally developed as a stand-alone application to visualize read alignments stored as binary versions of SAM (Sequence Alignment/Map) files and known as BAM files .  ... 
doi:10.1093/bioinformatics/btr703 pmid:22199388 pmcid:PMC3278759 fatcat:57t7vj3jn5c2rcb3uliyxjxnxy

COV2HTML: A Visualization and Analysis Tool of Bacterial Next Generation Sequencing (NGS) Data for Postgenomics Life Scientists

Marc Monot, Mickael Orgeur, Emilie Camiade, Clément Brehier, Bruno Dupuy
2014 Omics  
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  ...  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.  ...  Thierry Garnier for suggestions and commentsof the manuscript.This work was supported by Institut Pasteur and grant ERA-PTG/SAU/0002/2008 (ERA-NET PathoGenoMics) for Bruno Dupuy and Marc Monot.  ... 
doi:10.1089/omi.2013.0119 pmid:24512253 pmcid:PMC3934542 fatcat:4ic3av2mmbg23ckzj2yvkae6je

MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation

H. Hou, F. Zhao, L. Zhou, E. Zhu, H. Teng, X. Li, Q. Bao, J. Wu, Z. Sun
2010 Nucleic Acids Research  
In conclusion, MagicViewer is a sophisticated assembly visualization and genetic variation annotation tool for next-generation sequencing data, which can be widely used in a variety of sequencing-based  ...  To satisfy the impending need for deciphering the large-scale data generated from next-generation sequencing, an integrated software MagicViewer is developed to easily visualize short read mapping, identify  ...  BamView is a Java application designed for visualizing large amounts of short reads alignment with an input of BAM (Binary Alignment/Map) format (10) . inGAP, albeit not specifically designed for sequencing  ... 
doi:10.1093/nar/gkq302 pmid:20444865 pmcid:PMC2896176 fatcat:vckzrgfmlrcmbhullppt7utfja

VisVariant: A java program to visualise genetic variants in next-generation sequencing data [article]

King Wai Lau, Michelle Kleeman, Caroline Reuter, Attila Lorincz
2021 bioRxiv   pre-print
To help facilitate interpretation of genetic variant next-generation sequencing (NGS) data we developed VisVariant, a customizable visualization tool that creates a figure showing the overlapping sequence  ...  Intuitive visualization of genetic variants in genomic sequencing data could help in the review and confirmation process of variants called by automated variant calling programs.  ...  Introduction Next-generation sequencing (NGS) is fast becoming the de facto tool to identify genetic variants. Many variants can be found in one sequencing experiment.  ... 
doi:10.1101/2021.02.12.431037 fatcat:a72u6nqnrzdupajgh5w2eeuvjy

Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data

Ethan C. Rath, Stephanie Pitman, Kyu Hong Cho, Yongsheng Bai
2017 BMC Bioinformatics  
Using Artemis and Bamview genome viewers, these regions were visually verified leaving 6 putative sRNAs.  ...  Results: For this study, we created an RNase III null mutant of Streptococcus pyogenes and its RNA sequencing (RNA-Seq) data were analyzed and compared to that of the wild-type.  ...  The funding body was not involved with the design of the study, analysis, and interpretation of data or in the writing of the manuscript.  ... 
doi:10.1186/s12859-017-1897-0 pmid:29297355 pmcid:PMC5751559 fatcat:36zernq4ofbjjbedcdveca2f3y

Visualization and analysis of RNA-Seq assembly graphs

2019 Nucleic Acids Research  
Here we demonstrate the utility of this approach, including the unusual structure of these graphs and how they can be used to identify issues in assembly, repetitive sequences within transcripts and splice  ...  However, when the underlying transcript assemblies are complex, current visualization approaches can be limiting, with splicing events a challenge to interpret.  ...  INTRODUCTION The advent of next generation sequencing platforms enables new approaches to solving a variety of problems in medicine, agriculture, evolution and the environment.  ... 
doi:10.1093/nar/gkz599 pmid:31305886 pmcid:PMC6698738 fatcat:5dwszudnpvcklb3bdrtzougbvq

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

H. Thorvaldsdottir, J. T. Robinson, J. P. Mesirov
2012 Briefings in Bioinformatics  
A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic  ...  However, the size and diversity of the data sets produced by today's sequencing and array-based profiling methods present major challenges to visualization tools.  ...  INTRODUCTION Next-generation sequencing (NGS) and array-based profiling methods now generate large quantities of diverse types of genomic data and are enabling researchers to study the genome at unprecedented  ... 
doi:10.1093/bib/bbs017 pmid:22517427 pmcid:PMC3603213 fatcat:2su5wx7lsvbfdfo2lakowdwmuy

A survey of tools for variant analysis of next-generation genome sequencing data

S. Pabinger, A. Dander, M. Fischer, R. Snajder, M. Sperk, M. Efremova, B. Krabichler, M. R. Speicher, J. Zschocke, Z. Trajanoski
2013 Briefings in Bioinformatics  
Specifically, whole-exome sequencing using next-generation sequencing (NGS) technologies is gaining popularity in the human genetics community due to the moderate costs, manageable data amounts and straightforward  ...  interpretation of analysis results.  ...  Stand-alone applications 'Artemis' [135] incorporates BamView [136] for viewing aligned reads and is able to display different properties of a loaded sequence.  ... 
doi:10.1093/bib/bbs086 pmid:23341494 pmcid:PMC3956068 fatcat:zcunpg3i7bfrvhm5dixp6r6ofq

Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges

Natasha Andressa Nogueira Jorge, Carlos Gil Ferreira, Fabio Passetti
2012 Frontiers in Genetics  
In this review, we present and discuss bioinformatics advances in the development of computational approaches to analyze and discover ncRNA data in oncology using high throughput sequencing technologies  ...  The numerous genome sequencing projects produced unprecedented amount of data providing significant information to the discovery of novel non-coding RNA (ncRNA).  ...  Fabio Passetti and Carlos Gil Ferreira acknowledge the support of Fundação do Câncer.  ... 
doi:10.3389/fgene.2012.00287 pmid:23251139 pmcid:PMC3523245 fatcat:coi7jweukzb33nhvhbab4impmy

Dynamic Interactions Between the Genome and an Endogenous Retrovirus: Tirant in Drosophilasimulans Wild-Type Strains

Marie Fablet, Angelo Jacquet, Rita Rebollo, Annabelle Haudry, Carine Rey, Judit Salces-Ortiz, Prajakta Bajad, Nelly Burlet, Michael F. Jantsch, Maria Pilar García Guerreiro, Cristina Vieira
2019 G3: Genes, Genomes, Genetics  
Among these are endogenous retroviruses (ERVs), which are sequences similar to retroviruses and are transmitted across generations from parent to progeny.  ...  At the center of the epigenetic control of TEs are small interfering RNAs of the piRNA class, which trigger heterochromatinization of TE sequences.  ...  ACKNOWLEDGMENTS This work was performed using the computing facilities of the CC LBBE/PRABI, the luminometer of the IUT Lyon 1 Biology Department, and the Vienna Biocenter Campus Facility.  ... 
doi:10.1534/g3.118.200789 pmid:33575750 fatcat:ykdu4dmkxbgzxjfcbajptflthe

Evolutionary analysis of the most polymorphic gene family in falciparum malaria

Thomas D. Otto, Sammy A. Assefa, Ulrike Böhme, Mandy J. Sanders, Dominic Kwiatkowski, Matt Berriman, Chris Newbold, Pf3k consortium
2019 Wellcome Open Research  
level of sequence sharing both within and between continents.  ...  We also address the evolution of the var repertoire with respect to the ancestral genes within the Laverania and show that diversity generated by recombination is concentrated in a number of hotspots.  ...  We thank the staff of Wellcome Sanger Institute Sample Logistics, Sequencing, and Informatics facilities for their contribution.  ... 
doi:10.12688/wellcomeopenres.15590.1 pmid:32055709 pmcid:PMC7001760 fatcat:rdezvgo4ore33boykmkvb75ztm

Incorporating computational resources in a cancer research program

Nicholas T. Woods, Ankita Jhuraney, Alvaro N. A. Monteiro
2014 Human Genetics  
Thus, one of the most pressing issues facing an experimental cancer biology research program in genetics is incorporating data from multiple sources to annotate, visualize, and analyze the system under  ...  These advances have served as the basis for the generation of a number of richly annotated datasets relevant to the cancer geneticist.  ...  Acknowledgments Work in the Monteiro Lab is funded by NIH awards U19 CA148112 (GAME-ON consortium), U01 CA116167, R21 CA184996 (to N.W.) and by awards from the Moffitt Foundation.  ... 
doi:10.1007/s00439-014-1496-3 pmid:25324189 pmcid:PMC4401625 fatcat:gkrgo3kbsnag3hadp67q3pzqcq

Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution [article]

Aude Gilabert, Thomas Otto, Gavin Rutledge, Blaise Franzon, Benjamin Ollomo, Celine Arnathau, Patrick Durand, Nancy Moukodoum, Alain-Prince Okouga, Barthelemy Ngoubangoye, Boris Makanga, Larson Boudenga (+4 others)
2017 biorxiv/medrxiv   pre-print
To unravel the evolutionary history and adaptation of P. vivax, we generated using long and short read sequence technologies the two first P. vivax-like reference genomes and 9 additional P. vivax-like  ...  Analyses show that the genomes of P. vivax and P. vivax-like are highly similar and co-linear within the core regions.  ...  Authors thank Mandy Sanders, Chris Newbold, Matthew Berriman, and Frederic Delsuc for performing the sequencing and providing helpful discussion.  ... 
doi:10.1101/205302 fatcat:bvmhfcqmrjajxaeufbj7ikz3fm

Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution

Aude Gilabert, Thomas D. Otto, Gavin G. Rutledge, Blaise Franzon, Benjamin Ollomo, Céline Arnathau, Patrick Durand, Nancy D. Moukodoum, Alain-Prince Okouga, Barthélémy Ngoubangoye, Boris Makanga, Larson Boundenga (+5 others)
2018 PLoS Biology  
To unravel the evolutionary history and adaptation of P. vivax to different host environments, we generated using long-and short-read sequence technologies 2 new P. vivax-like reference genomes and 9 additional  ...  Analyses show that the genomes of P. vivax and P. vivax-like are highly similar and colinear within the core regions.  ...  Authors thank Mandy Sanders, Chris Newbold, Matthew Berriman, and Frederic Delsuc for performing the sequencing and providing helpful discussion.  ... 
doi:10.1371/journal.pbio.2006035 pmid:30142149 fatcat:pz5ifc3qord4lgdfcj6demnx6u
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