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A haplotype-aware de novo assembly of related individuals using pedigree graph
[article]
2019
bioRxiv
pre-print
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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]
2019
bioRxiv
pre-print
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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]
2020
arXiv
pre-print
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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
2018
Genome Biology
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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
2017
Nature
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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]
2021
bioRxiv
pre-print
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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]
2016
bioRxiv
pre-print
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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
2020
Nature Genetics
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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
2016
Bioinformatics
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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]
2016
bioRxiv
pre-print
Preserved Fulltext
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The file type is application/pdf.
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]
2016
biorxiv/medrxiv
pre-print
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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
Preserved Fulltext
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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
2014
Evolutionary Applications
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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
2020
Genome Biology
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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
2016
Genetics
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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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