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BamView: viewing mapped read alignment data in the context of the reference sequence

T. Carver, U. Bohme, T. D. Otto, J. Parkhill, M. Berriman
2010 Bioinformatics  
BamView has also been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features.  ...  BamView is an interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence.  ...  ACKNOWLEDGEMENTS We would like to thank Gary Dillon, Jacqui McQuillan, Anna Protasio for their suggestions in the development of this application.  ... 
doi:10.1093/bioinformatics/btq010 pmid:20071372 pmcid:PMC2828118 fatcat:ewjujt5lsbdcfpdhyaeb7mav4i

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  
As well as being a standalone application it can be used as an integrated part of the Artemis genome browser, BamView allows the user to study NGS data in the context of the sequence and annotation of  ...  To enable in-depth investigation of NGS data, various views are provided that can be configured to highlight interesting aspects of the data.  ...  alignments in the context of genome annotation.  ... 
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  ...  ACKNOWLEDGEMENTS We thank Kim Wong at the WTSI for providing feedback on the Mouse Genomes dataset.  ... 
doi:10.1093/bioinformatics/btr703 pmid:22199388 pmcid:PMC3278759 fatcat:57t7vj3jn5c2rcb3uliyxjxnxy

Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format

M. N. Edmonson, J. Zhang, C. Yan, R. P. Finney, D. M. Meerzaman, K. H. Buetow
2011 Bioinformatics  
The assembly viewer can display reads in the context of either a user-provided or automatically generated reference sequence, retrieve genome annotation features from a UCSC genome annotation database,  ...  Bambino is a variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files.  ...  Reference sequence alignment programs such as mapping and assembly with qualities (MAQ) and burrows-wheeler alignment tool (BWA) (Li et al., 2009b ) support SAM either directly or via conversion with  ... 
doi:10.1093/bioinformatics/btr032 pmid:21278191 pmcid:PMC3051333 fatcat:ygsmvpac3bevvdzztxzn53gu3m

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

H. Thorvaldsdottir, J. T. Robinson, J. P. Mesirov
2012 Briefings in Bioinformatics  
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.  ...  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  ...  Acknowledgements We thank the following collaborators for their contributions to components described in this manuscript:  ... 
doi:10.1093/bib/bbs017 pmid:22517427 pmcid:PMC3603213 fatcat:2su5wx7lsvbfdfo2lakowdwmuy

A survey of sequence alignment algorithms for next-generation sequencing

H. Li, N. Homer
2010 Briefings in Bioinformatics  
A central challenge to the analysis of this data is sequence alignment, whereby sequence reads must be compared to a reference.  ...  We come to the conclusion that short-read alignment is no longer the bottleneck of data analyses.  ...  Acknowledgements We thank the three anonymous reviewers whose comments helped us to improve the manuscript.  ... 
doi:10.1093/bib/bbq015 pmid:20460430 pmcid:PMC2943993 fatcat:p2qoot222zblhgylxjtmaihu54

Visualization and analysis of RNA-Seq assembly graphs

2019 Nucleic Acids Research  
Following the mapping of reads to a reference genome, a read-to-read comparison is performed on all reads mapping to a given gene, producing a weighted similarity matrix between reads.  ...  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  ...  It is also routine practice to port data into tools such as IGV, where they can be visualized in the context of the reference genome (where available).  ... 
doi:10.1093/nar/gkz599 pmid:31305886 pmcid:PMC6698738 fatcat:5dwszudnpvcklb3bdrtzougbvq

Standard operating procedure for somatic variant refinement of tumor sequencing data [article]

Erica K. Barnell, Peter Ronning, Katie M. Campbell, Kilannin Krysiak, Benjamin J. Ainscough, Cody Ramirez, Nick Spies, Jason Kunisaki, Jasreet Hundal, Zachary L. Skidmore, Felicia Gomez, Lee Trani (+5 others)
2018 bioRxiv   pre-print
Purpose: Manual review of aligned sequencing reads is required to develop a high-quality list of somatic variants from massively parallel sequencing data (MPS).  ...  The approach is enhanced through representative examples of 4 different manual review categories that indicate a reviewer's confidence in the somatic variant call and 19 annotation tags that contextualize  ...  A large number of artifacts arise from poor alignment of sequence reads to the reference genome.  ... 
doi:10.1101/266262 fatcat:d4tznxmywzb45n5oxucc6jcsq4

SeqTools: visual tools for manual analysis of sequence alignments

Gemma Barson, Ed Griffiths
2016 BMC Research Notes  
Manual annotation is essential to create high-quality reference alignments and annotation. Annotators need to be able to view sequence alignments in detail.  ...  Belvu is used to analyse conservation patterns in multiple sequence alignments and to perform a combination of manual and automatic processing of the alignment.  ...  Availabilty of supporting data The SeqTools programs are designed to be generic viewers of certain text file formats, such as GFF, FASTA and Stockholm.  ... 
doi:10.1186/s13104-016-1847-3 pmid:26801397 pmcid:PMC4724122 fatcat:z2gvtkeuzjbxdmta4fymrpi6vm

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  
At the center of the epigenetic control of TEs are small interfering RNAs of the piRNA class, which trigger heterochromatinization of TE sequences.  ...  Taken together, our results participate in the understanding of the equilibrium between the host genome and its TEs.  ...  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

GeneDB--an annotation database for pathogens

F. J. Logan-Klumpler, N. De Silva, U. Boehme, M. B. Rogers, G. Velarde, J. A. McQuillan, T. Carver, M. Aslett, C. Olsen, S. Subramanian, I. Phan, C. Farris (+16 others)
2011 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors wish to acknowledge the contribution of numerous members of the parasitology research community, in the form of advice, suggestions and/or data.  ...  Currently short-read alignments can be viewed using Artemis BAMview (5), and more recently pileup format files, converted to VCF, can now be viewed with Artemis VCFview.  ...  Here the focus has shifted away from the generation of new reference genomes, to the mapping of variant data to existing references.  ... 
doi:10.1093/nar/gkr1032 pmid:22116062 pmcid:PMC3245030 fatcat:4znikrcq3zbxjizxzokpcjullm

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

Georgios A. Pavlopoulos, Dimitris Malliarakis, Nikolas Papanikolaou, Theodosis Theodosiou, Anton J. Enright, Ioannis Iliopoulos
2015 GigaScience  
Although, in general, the notion of capturing complex ideas using images is very appealing, would 1000 words be enough to describe the unknown in a research field such as the life sciences?  ...  This widely used adage sums up in a few words the notion that a successful visual representation of a concept should enable easy and rapid absorption of large amounts of information.  ...  and pair-end short reads MultiPipMaker [217] Computes alignments of similar regions in two DNA sequences.  ... 
doi:10.1186/s13742-015-0077-2 pmid:26309733 pmcid:PMC4548842 fatcat:w7hxgunagfcbxctnio7kwnucsy

Whole genome sequencing and microsatellite analysis of the Plasmodium falciparum E5 NF54 strain show that the var, rifin and stevor gene families follow Mendelian inheritance

Ellen Bruske, Thomas D. Otto, Matthias Frank
2018 Malaria Journal  
This is the first time that VSA genes in sibling parasites were analysed with long read sequencing technology.  ...  Short and long read whole genome sequencing (WGS) techniques (Ilumina, Pacific Bioscience) and a set of 84 microsatellites (MS) were employed to characterize the 3D7 and non-3D7 parts of the E5 genome.  ...  Chris facilitated the sequencing of E5 and brought us (EB, MF and TO) together as scientists.  ... 
doi:10.1186/s12936-018-2503-2 pmid:30348135 pmcid:PMC6198375 fatcat:pnfpbwncmrgv3aovd76too3k4a

Comparative genomics of drug resistance in Trypanosoma brucei rhodesiense

Fabrice E. Graf, Philipp Ludin, Christian Arquint, Remo S. Schmidt, Nadia Schaub, Christina Kunz Renggli, Jane C. Munday, Jessica Krezdorn, Nicola Baker, David Horn, Oliver Balmer, Adalgisa Caccone (+2 others)
2016 Cellular and Molecular Life Sciences (CMLS)  
The finding that concomitant deletion of the known resistance genes AT1 and AQP2 in T. b. brucei failed to phenocopy the high levels of resistance of the T. b. rhodesiense mutants indicated a possible  ...  However, homozygous in situ expression of UBP1-Leu 131 in T. b. brucei did not affect the sensitivity to melarsoprol or pentamidine.  ...  Support for the STIB900 Illumina data was provided to the NIH R21 Grant AI094615-01 awarded to AC.  ... 
doi:10.1007/s00018-016-2173-6 pmid:26973180 pmcid:PMC4967103 fatcat:pcl62svulvbv3jvkfquv5ne2c4

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  
While whole-exome and, in the near future, whole-genome sequencing are becoming commodities, data analysis still poses significant challenges and led to the development of a plethora of tools supporting  ...  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  ...  Acknowledgements We thank the reviewers for their numerous constructive suggestions, which helped us to considerably improve the article.  ... 
doi:10.1093/bib/bbs086 pmid:23341494 pmcid:PMC3956068 fatcat:zcunpg3i7bfrvhm5dixp6r6ofq
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