TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Keywords

BiologyHuman geneticsGeneticsGeneTranscriptomeComputational biologyComputational genomicsGenome BiologyGenomicsEvolutionary biologyGenomeGene expression

Affiliated Institutions

Related Publications

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

Abstract Motivation Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic cont...

2018 Bioinformatics 14625 citations

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

Daehwan Kim , Joseph M. Paggi , Chanhee Park +2 more

The human reference genome represents only a small number of individuals, which limits its usefulness for genotyping. We present a method named HISAT2 (hierarchical indexing for...

2019 Nature Biotechnology 13675 citations

Genome-wide identification of chromosomal regions of increased tumor expression by transcriptome analysis.

Yan Zhou , Shiuh-Ming Luoh , Yan Zhang +5 more

Genes up-regulated in tumor cells provide attractive anticancer therapeutic targets. Although the general underlying mechanism for the increased expression in tumors is unknown,...

2003 PubMed 51 citations

De novo assembly of human genomes with massively parallel short read sequencing

Ruiqiang Li , Hongmei Zhu , Jue Ruan +11 more

Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length...

2009 Genome Research 2939 citations

Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner

Mathieu Blanchette , W. James Kent , Cathy Riemer +9 more

We define a “threaded blockset,” which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for “threaded blockset aligner...

2004 Genome Research 1541 citations

Publication Info

Year: 2013
Type: article
Volume: 14
Issue: 4
Pages: R36-R36
Citations: 13345
Access: Closed

External Links

View on DOI.org

Social Impact

Altmetric

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

13345

OpenAlex

Cite This

APA Style

                            
                                
                                    Daehwan Kim, 
                                
                                    Geo Pertea, 
                                
                                    Cole Trapnell
                                
                                et al.
                            
                            (2013). 
                            TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. 
                            Genome biology
                            , 14
                            (4)
                            , R36-R36.
                            https://doi.org/10.1186/gb-2013-14-4-r36
                        

Identifiers

DOI: 10.1186/gb-2013-14-4-r36