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

Kim, Daehwan; Paggi, Joseph M.; Park, Chanhee; Bennett, Christopher; Salzberg, Steven L.

doi:10.1038/s41587-019-0201-4

Cited by 9,103 publications

(6,360 citation statements)

References 37 publications

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“…The illumina data were first mapped to the adenovirus genome using HISAT2 (ref. 47 ) before using an in-house script (compare_nanopore_splices_to_illumina.pl) to determine which splice events identified by the nanopore data were also present in the illumina data.…”

Section: Methodsmentioning

confidence: 99%

Deep splicing plasticity of the human adenovirus type 5 transcriptome drives virus evolution

et al. 2020

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Viral genomes have high gene densities and complex transcription strategies rendering transcriptome analysis through short-read RNA-seq approaches problematic. Adenovirus transcription and splicing is especially complex. We used long-read direct RNA sequencing to study adenovirus transcription and splicing during infection. This revealed a previously unappreciated complexity of alternative splicing and potential for secondary initiating codon usage. Moreover, we find that most viral transcripts tend to shorten polyadenylation lengths as infection progresses. Development of an open reading frame centric bioinformatics analysis pipeline provided a deeper quantitative and qualitative understanding of adenovirus's genetic potential. Across the viral genome adenovirus makes multiple distinctly spliced transcripts that code for the same protein. Over 11,000 different splicing patterns were recorded across the viral genome, most occurring at low levels. This low-level use of alternative splicing patterns potentially enables the virus to maximise its coding potential over evolutionary timescales.

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Section: Methodsmentioning

confidence: 99%

Deep splicing plasticity of the human adenovirus type 5 transcriptome drives virus evolution

et al. 2020

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“…Read quality was assessed and adapters trimmed using fastp (Chen et al 2018). Reads were then mapped to either the mouse genome version mm10 (UCSC, Santa Cruz, CA, USA) or rat genome version rn6 (release 95, Ensembl, Cambridge, UK) using HISAT2 (Kim et al 2019). For comparison of mouse and rat datasets, we used the getLDS function of biomaRt (Durinck et al 2009) to find homologous annotated features between the two species.…”

Section: Rna Sequencingmentioning

confidence: 99%

Widespread diversity in the transcriptomes of functionally divergent limb tendons

Disser

Ghahramani

Swanson

et al. 2019

Preprint

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r Tendon is a hypocellular, matrix-rich tissue that has been excluded from comparative transcriptional atlases. These atlases have provided important knowledge about biological heterogeneity between tissues, and our study addresses this important gap.r We performed measures on four of the most studied tendons, the Achilles, forepaw flexor, patellar and supraspinatus tendons of both mice and rats. These tendons are functionally distinct and are also among the most commonly injured, and therefore of important translational interest.r Approximately one-third of the filtered transcriptome was differentially regulated between Achilles, forepaw flexor, patellar and supraspinatus tendons within either mice or rats. Nearly two-thirds of the transcripts that are expressed in anatomically similar tendons were different between mice and rats.r The overall findings from this study identified that although tendons across the body share a common anatomical definition based on their physical location between skeletal muscle and bone, tendon is a surprisingly genetically heterogeneous tissue.Abstract Tendon is a functionally important connective tissue that transmits force between skeletal muscle and bone. Previous studies have evaluated the architectural designs and mechanical properties of different tendons throughout the body. However, less is known about the underlying transcriptional differences between tendons that may dictate their designs and properties. Therefore, our objective was to develop a comprehensive atlas of the transcriptome of limb tendons in adult mice and rats using systems biology techniques. We selected the Achilles, forepaw digit flexor, patellar, and supraspinatus tendons due to their divergent functions and Nathaniel Disser graduated in 2018 from Gonzaga University in Spokane, WA, where he obtained a Bachelor of Science degree in Human Physiology. He is now participating in a two-year Post-Baccalaureate Research Program at the Hospital for Special Surgery in New York, NY. His current research interests include studying the mechanobiology of tendon and muscle during tissue growth and repair. As an aspiring physician-scientist, he hopes to improve the understanding and treatment of debilitating musculoskeletal injuries and diseases. N. P. Disser and others J Physiol 598.8 high rates of injury and tendinopathies in patients. Using RNA sequencing data, we generated the Comparative Tendon Transcriptional Database (CTTDb) that identified substantial diversity in the transcriptomes of tendons both within and across species. Approximately 30% of filtered transcripts were differentially regulated between tendons of a given species, and nearly 60% of the filtered transcripts present in anatomically similar tendons were different between species. Many of the genes that differed between tendons and across species are important in tissue specification and limb morphogenesis, tendon cell biology and tenogenesis, growth factor signalling, and production and maintenance of the extracellular matrix. This study indicate...

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“…Among others, this proposition has led to a paradigm shift from the usual linear representation of reference genomes to a representation as pangenome graphs bringing together all the different known variations as multiple alternative paths. Methods [19,20,21] have been developed aiming at factorizing pangenomes at the genome sequence-level to capture all the nucleotide variations in a graph that enables variant calling and improves the sensitivity of the read mapping (summarized in [22]).…”

Section: Introductionmentioning

confidence: 99%

PPanGGOLiN: depicting microbial diversity via a partitioned pangenome graph

Gautreau

Bazin

Gachet

et al. 2019

Preprint

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The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of occurrence in a given species. These methods usually lack multivariate statistical models to infer the partitions and the optimal number of classes and don't account for genome organization. We introduce a graph structure to model pangenomes in which nodes represent gene families and edges represent genomic neighborhood. Our method, named PPanGGOLiN, partitions nodes using an Expectation-Maximization algorithm based on multivariate Bernoulli Mixture Model coupled with a Markov Random Field. This approach takes into account the topology of the graph and the presence/absence of genes in pangenomes to classify gene families into persistent, cloud, and one or several shell partitions. By analyzing the partitioned pangenome graphs of isolate genomes from 439 species and metagenome-assembled genomes from 78 species, we demonstrate that our method is effective in estimating the persistent genome. Interestingly, it shows that the shell genome is a key element to understand genome dynamics, presumably because it reflects how genes present at intermediate frequencies drive adaptation of species, and its proportion in genomes is independent of genome size. The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative genomics. The software is freely available at https://github.com/labgem/PPanGGOLiN.

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

Cited by 9,103 publications

References 37 publications

Deep splicing plasticity of the human adenovirus type 5 transcriptome drives virus evolution

Deep splicing plasticity of the human adenovirus type 5 transcriptome drives virus evolution

Widespread diversity in the transcriptomes of functionally divergent limb tendons

PPanGGOLiN: depicting microbial diversity via a partitioned pangenome graph

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