{"doi":"10.1093/bioinformatics/bts443","title":"CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>Summary: To 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.</jats:p>\n               <jats:p>Availability: CBrowse is distributed under the GNU General Public License, available at http://bioinfolab.muohio.edu/CBrowse/</jats:p>\n               <jats:p>Contact:  liangc@muohio.edu or liangc.mu@gmail.com; glji@xmu.edu.cn</jats:p>\n               <jats:p>Supplementary Information:  Supplementary data are available at Bioinformatics online.</jats:p>","journal":"Bioinformatics","year":2012,"id":590042,"datarank":0.9046817482898954,"base_score":2.1972245773362196,"endowment":2.1972245773362196,"self_citation_contribution":0.32958368660043297,"citation_network_contribution":0.5750980616894625,"self_endowment_contribution":0.32958368660043297,"citer_contribution":0.5750980616894625,"corpus_percentile":null,"corpus_rank":null,"citation_count":8,"citer_count":7,"citers_with_citation_signal":6,"citers_with_endowment":6,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":491465,"name":"Guoli Ji","orcid":null,"position":1,"is_corresponding":false},{"id":1361864,"name":"Min Dong","orcid":"0000-0003-2263-1877","position":2,"is_corresponding":false},{"id":1129580,"name":"Emily Schmidt","orcid":"0000-0003-3436-4323","position":3,"is_corresponding":false},{"id":1509692,"name":"Douglas Lenox","orcid":null,"position":4,"is_corresponding":false},{"id":1353392,"name":"Liangliang Chen","orcid":"0000-0001-5740-7221","position":5,"is_corresponding":false},{"id":620561,"name":"Qi Liu","orcid":"0000-0001-6412-3286","position":6,"is_corresponding":false},{"id":1406403,"name":"Lin Liu","orcid":"0000-0002-9041-8296","position":7,"is_corresponding":false},{"id":529965,"name":"Jie Zhang","orcid":"0000-0002-1985-5485","position":8,"is_corresponding":false},{"id":258207,"name":"Chun Liang","orcid":"0000-0003-1996-6027","position":9,"is_corresponding":false},{"id":1372957,"name":"Pei Li","orcid":"0000-0001-7276-6337","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>Summary: To 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.</jats:p>\n               <jats:p>Availability: CBrowse is distributed under the GNU General Public License, available at http://bioinfolab.muohio.edu/CBrowse/</jats:p>\n               <jats:p>Contact:  liangc@muohio.edu or liangc.mu@gmail.com; glji@xmu.edu.cn</jats:p>\n               <jats:p>Supplementary Information:  Supplementary data are available at Bioinformatics online.</jats:p>","is_dataset_classified":null,"base_score":2.1972245773362196,"endowment":2.1972245773362196,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"22789590","pmcid":"PMC3436847","openalex_id":"https://openalex.org/W2153811153","authors":[],"funders":[{"funder_name":"NIGMS NIH HHS","grant_id":"1R15GM94732-1","title":null}],"total_grants":1,"fwci":0.4909,"citation_percentile":0.63532408,"influential_citations":0,"citation_trend":[{"year":2013,"count":1},{"year":2014,"count":2},{"year":2015,"count":1},{"year":2016,"count":1},{"year":2023,"count":2},{"year":2025,"count":1}],"oa_status":"bronze","license":null,"oa_locations":[{"url":"https://academic.oup.com/bioinformatics/article-pdf/28/18/2382/48881516/bioinformatics_28_18_2382.pdf","host_type":"journal"},{"url":"https://academic.oup.com/bioinformatics/article-pdf/28/18/2382/48881516/bioinformatics_28_18_2382.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/bioinformatics/bts443","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/22789590","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3436847","host_type":"repository"}],"fields_of_study":["Genomics and Phylogenetic Studies","Bioinformatics and Genomic Networks","Gene expression and cancer classification","Computer Graphics","Contig Mapping","Gene Expression Profiling","High-Throughput Nucleotide Sequencing","Internet","Sequence Analysis, DNA","Software"],"mesh_terms":["Computer Graphics","Software","Sequence Analysis, DNA","Internet","Contig Mapping","Gene Expression Profiling","High-Throughput Nucleotide Sequencing"],"keywords":["Contig","Visualization","Transcriptome","Computer science","Software","World Wide Web","Computational biology","Computer graphics (images)","Data mining","Biology","Genetics","Genome","Programming language","Gene"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-24T12:36:20.525091Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}