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PanCake: A Data Structure for Pangenomes

Corinna Ernst, Sven Rahmann, Marc Herbstritt
2013 German Conference on Bioinformatics  
We present a pangenome data structure ("PanCake") for sets of related genomes, based on bundling similar sequence regions into shared features, which are derived from genome-wide pairwise sequence alignments  ...  The PanCake data structure requires significantly less space than the sum of individual sequence files.  ...  Acknowledgements We thank Johannes Köster and Marcel Martin for helpful discussions and sharing their Python knowledge.  ... 
doi:10.4230/oasics.gcb.2013.35 dblp:conf/gcb/ErnstR13 fatcat:wagkc6eoufbmzbqobfwepdouwm

A Brief Review of Software Tools for Pangenomics

Jingfa Xiao, Zhewen Zhang, Jiayan Wu, Jun Yu
2015 Genomics, Proteomics & Bioinformatics  
Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis.  ...  genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements.  ...  It would be a waste if such data are left unused. Second, orthologous gene identification is a key step in pangenomic analysis.  ... 
doi:10.1016/j.gpb.2015.01.007 pmid:25721608 pmcid:PMC4411478 fatcat:k3wmxjhy5jfuzl66gk3xec45am

A Review of Pangenome Tools and Recent Studies [chapter]

G. S. Vernikos
2020 The Pangenome  
on such a pangenomic journey.  ...  Herein we will review, from practical and technical implementation, existing projects of pangenome analysis, with the aim of providing the reader with a snapshot of useful tools should they need to embark  ...  seq-seq-pan seq-seq-pan (Jandrasits et al. 2018 ) is a workflow for the sequential alignment of sequences to build a pangenome data structure and a whole-genome alignment. seqseq-pan builds a pangenome  ... 
doi:10.1007/978-3-030-38281-0_4 fatcat:pqmpmbqt6fbwdd3k2xwr75icpa

Pangenomics in Microbial and Crop Research: Progress, Applications, and Perspectives

Sumit Kumar Aggarwal, Alla Singh, Mukesh Choudhary, Aundy Kumar, Sujay Rakshit, Pardeep Kumar, Abhishek Bohra, Rajeev K. Varshney
2022 Genes  
To comprehensively capture the genetic diversity for improving plant performance, the pangenome concept is further extended from species to genus level by the inclusion of wild species, constituting a  ...  Characterization of pangenome has implications for both basic and applied research. The concept of pangenome has transformed the way biological questions are addressed.  ...  A.K. is grateful to CRP-Genomics for logistic support for pathogenomics programme at IARI, New Delhi.  ... 
doi:10.3390/genes13040598 pmid:35456404 pmcid:PMC9031676 fatcat:alwq5axfqfdupc4mkkkjygrtwu

seq-seq-pan: Building a computational pan-genome data structure on whole genome alignment [article]

Christine Jandrasits, Piotr W. Dabrowski, Stephan Fuchs, Bernhard Y. Renard
2017 bioRxiv   pre-print
There is a need for the representation of multiple sequences in a composite way that is compatible with existing data sources for annotation and suitable for established sequence analysis methods.  ...  We introduce seq-seq-pan, a framework that provides methods for adding or removing new genomes from a set of aligned genomes and uses these to construct a whole genome alignment.  ...  Acknowledgements We would like to thank Lena Fiebig and Walter Haas (Robert Koch Institute) for fruitful discussions and André Hennig and Kay Nieselt (University of Tübingen) for valuable feedback and  ... 
doi:10.1101/188904 fatcat:ezlliiwygncp5gq725ixox42wu

Interest of bacterial pangenome analyses in clinical microbiology

Hussein Anani, Rita Zgheib, Issam Hasni, Didier Raoult, Pierre-Edouard Fournier
2020 Microbial Pathogenesis  
Bacterial pangenome constitutes a powerful method for understanding the history of human bacteria and relating these findings to diagnosis in clinical microbiology laboratories in order to optimize patient  ...  In addition, for many of them, sequences from several strains of a given species are available, thus enabling to evaluate their genetic diversity and study their evolution.  ...  data) [68] .  ... 
doi:10.1016/j.micpath.2020.104275 pmid:32562810 fatcat:jevw3ku4uvethibt76hldoo7y4

seq-seq-pan: building a computational pan-genome data structure on whole genome alignment

Christine Jandrasits, Piotr W. Dabrowski, Stephan Fuchs, Bernhard Y. Renard
2018 BMC Genomics  
There is a need for the representation of multiple sequences in a composite way that is compatible with existing data sources for annotation and suitable for established sequence analysis methods.  ...  Results: We introduce seq-seq-pan, a framework that provides methods for adding or removing new genomes from a set of aligned genomes and uses these to construct a whole genome alignment.  ...  Acknowledgments We would like to thank Lena Fiebig and Walter Haas (Robert Koch Institute) for fruitful discussions and André Hennig and Kay Nieselt (University of Tübingen) for valuable feedback and insight  ... 
doi:10.1186/s12864-017-4401-3 pmid:29334898 pmcid:PMC5769345 fatcat:ehw2kvfmvncmvgrcalmha5twai

Computational pan-genomics: status, promises and challenges

2016 Briefings in Bioinformatics  
Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets.  ...  In this article, we generalize existing definitions and understand a pangenome as any collection of genomic sequences to be analyzed jointly or to be used as a reference.  ...  For example, PanCake [119] uses a graph-based structure to represent common genomic segments and uses a compressed multiple-alignmentbased representation in each node of the graph. Dilthey et al.  ... 
doi:10.1093/bib/bbw089 pmid:27769991 pmcid:PMC5862344 fatcat:zeeomxopezehvl44bnap76snyq

Computational Pan-Genomics: Status, Promises and Challenges [article]

Tobias Marschall, Manja Marz, Thomas Abeel, Louis Dijkstra, Bas E Dutilh, Ali Ghaffaari, Paul Kersey, Wigard Kloosterman, Veli Makinen, Adam Novak, Benedict Paten, David Porubsky (+47 others)
2016 biorxiv/medrxiv   pre-print
As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs.  ...  Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic datasets.  ...  For example, PanCake [119] uses a graph-based structure to represent common genomic segments and uses a compressed multiple-alignmentbased representation in each node of the graph. Dilthey et al.  ... 
doi:10.1101/043430 fatcat:fhuu62lklndwtgct7d6qvxlsoi

Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage

Guillaume Holley, Roland Wittler, Jens Stoye
2016 Algorithms for Molecular Biology  
Conclusion: We present a novel succinct data structure called the Bloom Filter Trie for indexing a pan-genome as a colored de Bruijn graph.  ...  Results: In this paper, we present an alignment-free, reference-free and incremental data structure for storing a pan-genome as a C-DBG: the bloom filter trie (BFT).  ...  Acknowledgements The authors wish to thank the authors of SBT for helpful comments. GH and RW are funded by the International DFG Research Training Group GRK 1906/1.  ... 
doi:10.1186/s13015-016-0066-8 pmid:27087830 pmcid:PMC4832552 fatcat:lq53wnopvzervovgmq2auohryu

Bloom Filter Trie – A Data Structure for Pan-Genome Storage [chapter]

Guillaume Holley, Roland Wittler, Jens Stoye
2015 Lecture Notes in Computer Science  
In this paper, we present an alignment-free, reference-free and incremental data structure for storing a pan-genome as a C-DBG: the Bloom Filter Trie.  ...  The data structure allows to store and compress a set of colored k-mers, and also to efficiently traverse the graph.  ...  The authors wish to thank the anonymous reviewers and the authors of SBT for helpful comments. GH and RW are funded by the International DFG Research Training Group GRK 1906/1.  ... 
doi:10.1007/978-3-662-48221-6_16 fatcat:esvzdqqy35c55k3bnr53svurmq