ArticleBioinformatics (Oxford, England)2012
CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
5 citing papers in PubMed.
- Can ploidy changes propel the evolution of allogamy in a selfing species complex?BMC plant biology · 2025Article
- Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.GigaScience · 2015Review
- Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes.Frontiers in genetics · 2015Review
- RNAbrowse: RNA-Seq de novo assembly results browser.PloS one · 2014Article
- afterParty: turning raw transcriptomes into permanent resources.BMC bioinformatics · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
summaryTo address the impending need for exploring rapidly increased transcriptomics data generated for non-model organisms, we developed CBrowse, an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. Designed in a standard three-tier architecture with a data pre-processing pipeline, CBrowse is essentially a Rich Internet Application that offers many seamlessly integrated web interfaces and allows users to navigate, sort, filter, search and visualize data smoothly. The pre-processing pipeline takes the contig sequence file in FASTA format and its relevant SAM/BAM file as the input; detects putative polymorphisms, simple sequence repeats and sequencing errors in contigs and generates image, JSON and database-compatible CSV text files that are directly utilized by different web interfaces. CBowse is a generic visualization and analysis tool that facilitates close examination of assembly quality, genetic polymorphisms, sequence repeats and/or sequencing errors in transcriptome sequencing projects. AVAILABILITY: CBrowse is distributed under the GNU General Public License, available at http://bioinfolab.muohio.edu/CBrowse/ CONTACT: liangc@muohio.edu or liangc.mu@gmail.com; glji@xmu.edu.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.