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A haplotype-aware de novo assembly of related individuals using pedigree graph [article]

Shilpa Garg, John Aach, Heng Li, Richard Durbin, George Church
2019 bioRxiv   pre-print
genomics community.ResultsWe present a novel pedigree-graph-based approach to diploid assembly using accurate Illumina data and long-read Pacific Biosciences (PacBio) data from all related individuals  ...  Thus, building a trio-aware assembler capable of producing accurate and chromosomal-scale diploid genomes in a pedigree, while being cost-effective in terms of sequencing costs, is a pressing need of the  ...  Funding Conflict of Interest. GMC is the founder and holds leadership positions of many companies http://arep.med.harvard.edu/gmc/tech. html.  ... 
doi:10.1101/580159 fatcat:ljxpss5nsrayjcfvqmjd5bzgma

Detection of simple and complex de novo mutations without, with, or with multiple reference sequences [article]

Kiran V Garimella, Zamin Iqbal, Michael Krause, Susana Campino, Mihir Kekre, Eleanor Drury, Dominic Kwiatkowski, Juliana M Sa, Thomas E Wellems, Gil McVean
2019 bioRxiv   pre-print
The characterization of de novo mutations in regions of high sequence and structural diversity from whole genome sequencing data remains highly challenging.  ...  Complex structural variants tend to arise in regions of high repetitiveness and low complexity, challenging both de novo assembly, where short-reads do not capture the long-range context required for resolution  ...  First, de novo assembly, based on multicolor linked de Bruijn graphs, or LdBGs, is used to store and link adjacent k-mers for each sample.  ... 
doi:10.1101/698910 fatcat:6ededr7dzffljekankcmw6hdxq

Haplotype-resolved de novo assembly with phased assembly graphs [article]

Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng, Haowen Zhang, Heng Li
2020 arXiv   pre-print
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome.  ...  Here we describe hifiasm, a new de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph.  ...  Acknowledgements This study was supported by US National Institutes of Health (grant R01HG010040, U01HG010971 and U41HG010972 to H.L.). 9/11 Code availability Hifiasm is available at https://github.com  ... 
arXiv:2008.01237v1 fatcat:svfovmqhhnekbpizalb4nx4mfq

Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery

Heewook Lee, Carl Kingsford
2018 Genome Biology  
We have developed a graph-guided assembly technique for classical HLA genes, which can construct allele sequences given high-coverage whole-genome sequencing data.  ...  Our method delivers highly accurate HLA typing, comparable to the current state-of-the-art methods. Using various data, we also demonstrate that our method can type novel alleles.  ...  Availability of data and materials The WGS data for Illumina Platinum Genomes (17 individuals from CEPH/Utah pedigree 1463) are available from the European Nucleotide Archive under accession PRJEB3381  ... 
doi:10.1186/s13059-018-1388-2 pmid:29415772 pmcid:PMC5804087 fatcat:unnww2jscnbixjwp5you2gficq

Genomic innovation for crop improvement

Michael W. Bevan, Cristobal Uauy, Brande B. H. Wulff, Ji Zhou, Ksenia Krasileva, Matthew D. Clark
2017 Nature  
Advances in genome sequencing and assembly are being used to access to the large and complex genomes of crops and their wild relatives.  ...  Sequencing of wild crop relatives is identifying a wide spectrum of genetic variation, permitting the association of genetic diversity with diverse agronomic phenotypes.  ...  The DISCOVAR de novo genome assembler 27 captures a wider range of sequence variation during assembly by preserving sequence differences in the assembly graph.  ... 
doi:10.1038/nature22011 pmid:28300107 fatcat:rvnfxizclve2bjo42hnt3st6cq

Bovine pangenome reveals trait-associated structural variation from diverse assembly inputs [article]

Alexander S. Leonard, Danang Crysnanto, Zih-Hua Fang, Michael P Heaton, Brian L. Vander Ley, Carolina Herrera, Heinrich Bollwein, Derek M. Bickhart, Kristen L. Kuhn, Timothy PL. Smith, Benjamin D. Rosen, Hubert Pausch
2021 bioRxiv   pre-print
Ten haplotype-resolved assemblies of three bovine trios representing increasing levels of heterozygosity were generated that each demonstrate a substantial improvement in contiguity and accuracy over the  ...  However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated.  ...  These cases highlight the benefits of de novo, haplotype-resolved assemblies and pangenome integration.  ... 
doi:10.1101/2021.11.02.466900 fatcat:lscxfnry4jg5xkzcvw7fy7jaw4

trio-sga: facilitating de novo assembly of highly heterozygous genomes with parent-child trios [article]

Milan Malinsky, Jared T Simpson, Richard Durbin
2016 bioRxiv   pre-print
Two of the algorithms use haplotype phase information present in the trio data to eliminate the majority of heterozygous sites before the assembly commences.  ...  The high density of differences between the maternally and paternally contributed sequences (heterozygous sites) in some organisms makes de novo genome assembly very challenging, even for algorithms specifically  ...  We thank the Sanger Institute core facilities for sequencing.  ... 
doi:10.1101/051516 fatcat:nesxh24b35a4vlycgncn4n76mu

Haplotype-resolved genome analyses of a heterozygous diploid potato

Qian Zhou, Dié Tang, Wu Huang, Zhongmin Yang, Yu Zhang, John P. Hamilton, Richard G. F. Visser, Christian W. B. Bachem, C. Robin Buell, Zhonghua Zhang, Chunzhi Zhang, Sanwen Huang
2020 Nature Genetics  
Here, we report the 1.67-Gb haplotype-resolved assembly of a diploid potato, RH89-039-16, using a combination of multiple sequencing strategies, including circular consensus sequencing.  ...  This study offers a holistic view of the genome organization of a clonally propagated diploid species and provides insights into technological evolution in resolving complex genomes.  ...  Data availability The final RH genome assembly (RHgv3), annotation and a genome browser are available at Spud DB (https://solanaceae.plantbiology.msu.edu/rh_potato_ download.shtml/).  ... 
doi:10.1038/s41588-020-0699-x pmid:32989320 pmcid:PMC7527274 fatcat:vf6jzzafsrd3xgrfflblvxdr74

Read-based phasing of related individuals

Shilpa Garg, Marcel Martin, Tobias Marschall
2016 Bioinformatics  
inheritance to infer haplotypes within a pedigree of individuals.  ...  Combining both into an approach that uses these two independent sources of information-reads and pedigree-has the potential to deliver results better than each individually.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btw276 pmid:27307622 pmcid:PMC4908360 fatcat:opxujcjvqvadpp4rq6zvm44xzq

Read-Based Phasing of Related Individuals [article]

Shilpa Garg, Marcel Martin, Tobias Marschall
2016 bioRxiv   pre-print
inheritance to infer haplotypes within a pedigree of individuals.  ...  Combining both into an approach that uses these two independent sources of information -- reads and pedigree -- has the potential to deliver results better than each individually.  ...  Funding MM is supported by a grant from the Knut and Alice Wallenberg Foundation to the Wallenberg Advanced Bioinformatics Infrastructure.  ... 
doi:10.1101/037101 fatcat:nc6lwdxzqjchndfkyvregrqc3i

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.  ...  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.  ...  Another tool, Bandage [154] , visualizes de novo assembly graphs specifically. A number of challenges exist moving forward.  ... 
doi:10.1101/043430 fatcat:fhuu62lklndwtgct7d6qvxlsoi

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.  ...  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.  ...  Another tool, Bandage [154] , visualizes de novo assembly graphs specifically. A number of challenges exist moving forward.  ... 
doi:10.1093/bib/bbw089 pmid:27769991 pmcid:PMC5862344 fatcat:zeeomxopezehvl44bnap76snyq

A field guide to whole-genome sequencing, assembly and annotation

Robert Ekblom, Jochen B. W. Wolf
2014 Evolutionary Applications  
It is now within reach for individual research groups in the eco-evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice.  ...  Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to  ...  We also wish to thank all participants of the EBC Next Generation Sequencing Journal Club (Uppsala University) for stimulating discussions on this subject over several years.  ... 
doi:10.1111/eva.12178 pmid:25553065 pmcid:PMC4231593 fatcat:q466jassynd5jco7yxzzicjk4e

Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery

Danang Crysnanto, Hubert Pausch
2020 Genome Biology  
The current bovine genomic reference sequence was assembled from a Hereford cow.  ...  High nucleotide diversity and the separation of individuals by hundreds of breeds make cattle ideally suited to investigate the optimal composition of variation-aware references.  ...  We thank Braunvieh Schweiz for providing pedigree and genotype data of Original Braunvieh and Brown Swiss cattle. Semen samples of the sequenced bulls were kindly provided by Swissgenetics.  ... 
doi:10.1186/s13059-020-02105-0 pmid:32718320 fatcat:d5yvcjrigfgk5d35qzr6idwe4e

The Evolutionary Fates of a Large Segmental Duplication in Mouse

Andrew P. Morgan, J. Matthew Holt, Rachel C. McMullan, Timothy A. Bell, Amelia M.-F. Clayshulte, John P. Didion, Liran Yadgary, David Thybert, Duncan T. Odom, Paul Flicek, Leonard McMillan, Fernando Pardo-Manuel de Villena
2016 Genetics  
Given a seed ---mer present in that string set, this property can be exploited to 615 rapidly construct a de Bruijn graph which can in turn be used for local de novo assembly of a target 616 sequence (  ...  Using novel computational tools built around 71 indexes of raw high---throughput sequencing reads, we perform local de novo assembly of phased 72 haplotypes and explore patterns of sequence diversity within  ...  This 1221 allows rapid construction of a local de Bruijn graph starting from a ---mer seed (dark blue) and extending 1222 by successive ---mers (light blue) containing the ( − 1)---length suffix of the  ... 
doi:10.1534/genetics.116.191007 pmid:27371833 pmcid:PMC5012392 fatcat:alq5rb2i5re55nlflnvmps55nq
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