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A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference [article]

Sorina Maciuca, Carlos del Ojo Elias, Gil McVean, Zamin Iqbal
2016 bioRxiv   pre-print
We show how positional markers can be used to encode genetic variation within a Burrows-Wheeler Transform (BWT), and use this to construct a generalisation of the traditional 'reference genome', incorporating  ...  Our goal is to support the inference of the closest mosaic of previously known sequences to the genome(s) under analysis.  ...  We would like to thank Jacob Almagro-Garcia, Phelim Bradley, Rayan Chikhi, Simon Gog, Lin Huang, Jerome Kelleher, Heng Li, Gerton Lunter, Rachel Norris, Victoria Popic, and Jouni Siren for discussions  ... 
doi:10.1101/059170 fatcat:y75zskexsbgyjo62cfukdtwhd4

A Natural Encoding of Genetic Variation in a Burrows-Wheeler Transform to Enable Mapping and Genome Inference [chapter]

Sorina Maciuca, Carlos del Ojo Elias, Gil McVean, Zamin Iqbal
2016 Lecture Notes in Computer Science  
We show how positional markers can be used to encode genetic variation within a Burrows-Wheeler Transform (BWT), and use this to construct a generalisation of the traditional "reference genome", incorporating  ...  Our goal is to support the inference of the closest mosaic of previously known sequences to the genome(s) under analysis.  ...  We would like to thank Jacob Almagro-Garcia, Phelim Bradley, Rayan Chikhi, Simon Gog, Lin Huang, Jerome Kelleher, Heng Li, Gerton Lunter, Rachel Norris, Victoria Popic, and Jouni Siren for discussions  ... 
doi:10.1007/978-3-319-43681-4_18 fatcat:kiksaij2s5ashhypn75sj64pyi

An improved encoding of genetic variation in a Burrows-Wheeler transform [article]

Thomas Buechler, Enno Ohlebusch
2019 bioRxiv   pre-print
In a different approach, Maciuca et al. (2016) provided a 'natural encoding' of SNPs and other genetic variations in a BWT.  ...  Currently dominant read mappers (Li and Durbin, 2009; Langmead and Salzberg, 2012) are based on the Burrows-Wheeler transform (BWT).  ...  Discussion We have presented a new method to encode genetic variation in a Burrows-Wheeler transform, which extends the work of Huang et al. (2013) and Maciuca et al. (2016) in several aspects.  ... 
doi:10.1101/658716 fatcat:7govp2jpwfe4bjxs5f3qdq4ypi

Computational pan-genomics: status, promises and challenges

2016 Briefings in Bioinformatics  
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.  ...  Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes.  ...  In particular, we like to thank the Lorentz Center staff, who turned organizing and attending the workshop into a great pleasure.  ... 
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
In this paper, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference.  ...  Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes.  ...  There is also a special Burrows-Wheeler transform and an index based on that for a sequence graph [132, 133] .  ... 
doi:10.1101/043430 fatcat:fhuu62lklndwtgct7d6qvxlsoi

Sensitive and fast mapping of di-base encoded reads

F. Hormozdiari, F. Hach, S. C. Sahinalp, E. E. Eichler, C. Alkan
2011 Bioinformatics  
Motivation: Discovering variation among high-throughput sequenced genomes relies on efficient and effective mapping of sequence reads.  ...  , including segmental duplications, and is able to return all possible map locations and underlying sequence variation of short reads within a user-specified distance threshold.  ...  Funding: Natural Sciences and Engineering Research Council of Canada (NSERC to S.C.S. in parts); Bioinformatics for Combating Infectious Diseases (BCID to S.C.S. in parts); Michael Smith Foundation for  ... 
doi:10.1093/bioinformatics/btr303 pmid:21586516 pmcid:PMC3129524 fatcat:3pl3auezdbcg7hl7q6rlizptoe

Sensitive and fast mapping of di-base encoded reads

F. Hormozdiari, F. Hach, S. C. Sahinalp, E. E. Eichler, C. Alkan
2011 Bioinformatics  
Motivation: Discovering variation among high-throughput sequenced genomes relies on efficient and effective mapping of sequence reads.  ...  , including segmental duplications, and is able to return all possible map locations and underlying sequence variation of short reads within a user-specified distance threshold.  ...  Funding: Natural Sciences and Engineering Research Council of Canada (NSERC to S.C.S. in parts); Bioinformatics for Combating Infectious Diseases (BCID to S.C.S. in parts); Michael Smith Foundation for  ... 
doi:10.1093/bioinformatics/btr647 pmcid:PMC3276229 fatcat:rhah2ss57nbnlnahei4vubil5y

Genome graphs and the evolution of genome inference

Benedict Paten, Adam M. Novak, Jordan M. Eizenga, Erik Garrison
2017 Genome Research  
We thank David Haussler, Richard Durbin, Gil McVean, and members of the reference-genomes task team of the Global Alliance for Genomics and Health for many useful discussions.  ...  We thank Glenn Hickey, Charles Markello, Yohei Rosen, Eric Dawson, Mike Lin, and all contributors to the vg software package, which is driving much of our work forward.  ...  In linear references, the Positional Burrows-Wheeler Transform (PBWT) was developed in response to this challenge.  ... 
doi:10.1101/gr.214155.116 pmid:28360232 pmcid:PMC5411762 fatcat:hnzivagd3vef5jro7dsyc55eky

Graphical Pangenomics

Erik Garrison, Richard Durbin
2018 Zenodo  
To do so I formalize the concept of a variation graph to link genomes to a graphical model of their mutual alignment that is capable of representing any kind of genomic variation, both small and large.  ...  As this model combines both sequence and variation information in one structure it serves as a natural basis for resequencing.  ...  the Burrows-Wheeler Transform (BWT) [28] .  ... 
doi:10.5281/zenodo.1463032 fatcat:e65awps6hbav5gczb3ubrf65oi

Graphical pangenomics

Erik Garrison, Richard Durbin
2018 Zenodo  
To do so I formalize the concept of a variation graph to link genomes to a graphical model of their mutual alignment that is capable of representing any kind of genomic variation, both small and large.  ...  As this model combines both sequence and variation information in one structure it serves as a natural basis for resequencing.  ...  sibling the Burrows-Wheeler Transform (BWT) [28] .  ... 
doi:10.5281/zenodo.3269840 fatcat:glracsk2jvgb3lehvepq2jl5l4

Computational solutions for omics data

Bonnie Berger, Jian Peng, Mona Singh
2013 Nature reviews genetics  
Fortunately, an arsenal of algorithmic ideasapplicable in a wide variety of biological settings -can be deployed to address these challenges.  ...  In the past two decades, improvements in genomic sequencing capability have led to an exponential growth in the amount of publicly available sequence data that far outstrips the  ...  Acknowledgments The authors thank and L. Cowen for valuable feedback. B.B. thanks the US National Institutes of Health (NIH) for grant GM081871.  ... 
doi:10.1038/nrg3433 pmid:23594911 pmcid:PMC3966295 fatcat:b7n6xwzyc5gqzo7plgyoe257iq

Complex modifier landscape underlying genetic background effects

Jing Hou, Guihong Tan, Gerald R. Fink, Brenda J. Andrews, Charles Boone
2019 Proceedings of the National Academy of Sciences of the United States of America  
Here, in addition to confirming that some conditional essential genes are modified by a nonchromosomal element, we show that most cases involve a complex set of genomic modifiers.  ...  In natural yeast isolates, we found that the CYS3/CYS4 conditional essentiality can be caused by variation in two independent modifiers, MET1 and OPT1, each with roles associated with cellular cysteine  ...  The authors declare no conflict of interest.  ... 
doi:10.1073/pnas.1820915116 fatcat:7qcuxjentzajnddsdtdgcjara4

Genome Graphs and the Evolution of Genome Inference [article]

Benedict Paten, Adam M Novak, Jordan M Eizenga, Erik Garrison
2017 bioRxiv   pre-print
Here, we survey various projects underway to build and apply these graph based structures—which we collectively refer to as genome graphs—and discuss the improvements in read mapping, variant calling,  ...  However, because it excludes a great deal of common human variation, it introduces a pervasive reference bias into the field of human genomics.  ...  Disclosure Declaration The authors of this manuscript include authors of the vg Garrison (2016) and Glia tools described above. The authors declare no other conflicts of interest.  ... 
doi:10.1101/101816 fatcat:2kpmyq4fvfhdzjrgeegduufoky

Inferring whole-genome histories in large population datasets

Jerome Kelleher, Yan Wong, Anthony W. Wohns, Chaimaa Fadil, Patrick K. Albers, Gil McVean
2019 Nature Genetics  
Inferring the full genealogical history of a set of DNA sequences is a core problem in evolutionary biology, because this history encodes information about the events and forces that have influenced a  ...  We apply the method to human data from the 1000 Genomes Project, Simons Genome Diversity Project and UK Biobank, showing that the inferred genealogies are rich in biological signal and efficient to process  ...  Computation used the Oxford Biomedical Research Computing (BMRC) facility, a joint development between the Wellcome Centre for Human Genetics and the Big Data Institute supported by Health Data Research  ... 
doi:10.1038/s41588-019-0483-y pmid:31477934 pmcid:PMC6726478 fatcat:kjs5lushcrfjbikx5glygf2why

Reference-based phasing using the Haplotype Reference Consortium panel

Po-Ru Loh, Petr Danecek, Pier Francesco Palamara, Christian Fuchsberger, Yakir A Reshef, Hilary K Finucane, Sebastian Schoenherr, Lukas Forer, Shane McCarthy, Goncalo R Abecasis, Richard Durbin, Alkes L Price
2016 Nature Genetics  
Reference Consortium, HRC) using a new data structure based on the positional Burrows-Wheeler transform.  ...  Haplotype phasing is a fundamental problem in medical and population genetics.  ...  (a) We use the positional Burrows-Wheeler transform[19] to generate a "hedge" of haplotype prefix trees rooted at markers spaced across the chromosome.  ... 
doi:10.1038/ng.3679 pmid:27694958 pmcid:PMC5096458 fatcat:ojaubddehfga3chlly7tkzmd2y
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