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  1. Article ; Online: High-quality metagenome assembly from long accurate reads with metaMDBG.

    Benoit, Gaëtan / Raguideau, Sébastien / James, Robert / Phillippy, Adam M / Chikhi, Rayan / Quince, Christopher

    Nature biotechnology

    2024  

    Abstract: We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over sequences of minimizers to address variations in genome coverage depth and an ... ...

    Abstract We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over sequences of minimizers to address variations in genome coverage depth and an abundance-based filtering strategy to simplify strain complexity. For complex communities, we obtained up to twice as many high-quality circularized prokaryotic metagenome-assembled genomes as existing methods and had better recovery of viruses and plasmids.
    Language English
    Publishing date 2024-01-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1311932-1
    ISSN 1546-1696 ; 1087-0156
    ISSN (online) 1546-1696
    ISSN 1087-0156
    DOI 10.1038/s41587-023-01983-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation.

    Kille, Bryce / Garrison, Erik / Treangen, Todd J / Phillippy, Adam M

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Motivation: The Jaccard similarity on : Results: To address this, we propose ... ...

    Abstract Motivation: The Jaccard similarity on
    Results: To address this, we propose the
    Language English
    Publishing date 2023-05-18
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.05.16.540882
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets.

    Kille, Bryce / Nute, Michael G / Huang, Victor / Kim, Eddie / Phillippy, Adam M / Treangen, Todd J

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Motivation: Since 2016, the number of microbial species with available reference genomes in NCBI has more than tripled. Multiple genome alignment, the process of identifying nucleotides across multiple genomes which share a common ancestor, is used as ... ...

    Abstract Motivation: Since 2016, the number of microbial species with available reference genomes in NCBI has more than tripled. Multiple genome alignment, the process of identifying nucleotides across multiple genomes which share a common ancestor, is used as the input to numerous downstream comparative analysis methods. Parsnp is one of the few multiple genome alignment methods able to scale to the current era of genomic data; however, there has been no major release since its initial release in 2014.
    Results: To address this gap, we developed Parsnp v2, which significantly improves on its original release. Parsnp v2 provides users with more control over executions of the program, allowing Parsnp to be better tailored for different use-cases. We introduce a partitioning option to Parsnp, which allows the input to be broken up into multiple parallel alignment processes which are then combined into a final alignment. The partitioning option can reduce memory usage by over 4x and reduce runtime by over 2x, all while maintaining a precise core-genome alignment. The partitioning workflow is also less susceptible to complications caused by assembly artifacts and minor variation, as alignment anchors only need to be conserved within their partition and not across the entire input set. We highlight the performance on datasets involving thousands of bacterial and viral genomes.
    Availability: Parsnp is available at https://github.com/marbl/parsnp.
    Language English
    Publishing date 2024-01-31
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.30.577458
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: New advances in sequence assembly.

    Phillippy, Adam M

    Genome research

    2017  Volume 27, Issue 5, Page(s) xi–xiii

    MeSH term(s) Animals ; Genome, Human ; Humans ; Sequence Analysis, DNA/methods ; Sequence Analysis, DNA/trends ; Software
    Language English
    Publishing date 2017
    Publishing country United States
    Document type Editorial
    ZDB-ID 1284872-4
    ISSN 1549-5469 ; 1088-9051 ; 1054-9803
    ISSN (online) 1549-5469
    ISSN 1088-9051 ; 1054-9803
    DOI 10.1101/gr.223057.117
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation.

    Kille, Bryce / Garrison, Erik / Treangen, Todd J / Phillippy, Adam M

    Bioinformatics (Oxford, England)

    2023  Volume 39, Issue 9

    Abstract: Motivation: The Jaccard similarity on k-mer sets has shown to be a convenient proxy for sequence identity. By avoiding expensive base-level alignments and comparing reduced sequence representations, tools such as MashMap can scale to massive numbers of ... ...

    Abstract Motivation: The Jaccard similarity on k-mer sets has shown to be a convenient proxy for sequence identity. By avoiding expensive base-level alignments and comparing reduced sequence representations, tools such as MashMap can scale to massive numbers of pairwise comparisons while still providing useful similarity estimates. However, due to their reliance on minimizer winnowing, previous versions of MashMap were shown to be biased and inconsistent estimators of Jaccard similarity. This directly impacts downstream tools that rely on the accuracy of these estimates.
    Results: To address this, we propose the minmer winnowing scheme, which generalizes the minimizer scheme by use of a rolling minhash with multiple sampled k-mers per window. We show both theoretically and empirically that minmers yield an unbiased estimator of local Jaccard similarity, and we implement this scheme in an updated version of MashMap. The minmer-based implementation is over 10 times faster than the minimizer-based version under the default ANI threshold, making it well-suited for large-scale comparative genomics applications.
    Availability and implementation: MashMap3 is available at https://github.com/marbl/MashMap.
    MeSH term(s) Genomics ; Computational Biology
    Language English
    Publishing date 2023-08-19
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btad512
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs.

    Benoit, Gaëtan / Raguideau, Sébastien / James, Robert / Phillippy, Adam M / Chikhi, Rayan / Quince, Christopher

    bioRxiv : the preprint server for biology

    2023  

    Abstract: We introduce a novel metagenomics assembler for high-accuracy long reads. Our approach, implemented as metaMDBG, combines highly efficient de Bruijn graph assembly in minimizer space, with both a multi- ...

    Abstract We introduce a novel metagenomics assembler for high-accuracy long reads. Our approach, implemented as metaMDBG, combines highly efficient de Bruijn graph assembly in minimizer space, with both a multi-
    Language English
    Publishing date 2023-07-08
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.07.07.548136
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Improved sequence mapping using a complete reference genome and lift-over.

    Chen, Nae-Chyun / Paulin, Luis F / Sedlazeck, Fritz J / Koren, Sergey / Phillippy, Adam M / Langmead, Ben

    Nature methods

    2023  Volume 21, Issue 1, Page(s) 41–49

    Abstract: Complete, telomere-to-telomere (T2T) genome assemblies promise improved analyses and the discovery of new variants, but many essential genomic resources remain associated with older reference genomes. Thus, there is a need to translate genomic features ... ...

    Abstract Complete, telomere-to-telomere (T2T) genome assemblies promise improved analyses and the discovery of new variants, but many essential genomic resources remain associated with older reference genomes. Thus, there is a need to translate genomic features and read alignments between references. Here we describe a method called levioSAM2 that performs fast and accurate lift-over between assemblies using a whole-genome map. In addition to enabling the use of several references, we demonstrate that aligning reads to a high-quality reference (for example, T2T-CHM13) and lifting to an older reference (for example, Genome reference Consortium (GRC)h38) improves the accuracy of the resulting variant calls on the old reference. By leveraging the quality improvements of T2T-CHM13, levioSAM2 reduces small and structural variant calling errors compared with GRC-based mapping using real short- and long-read datasets. Performance is especially improved for a set of complex medically relevant genes, where the GRC references are lower quality.
    MeSH term(s) Sequence Analysis, DNA/methods ; Genome ; Genomics/methods ; Chromosome Mapping ; High-Throughput Nucleotide Sequencing
    Language English
    Publishing date 2023-11-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-023-02069-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps.

    Vollger, Mitchell R / Kerpedjiev, Peter / Phillippy, Adam M / Eichler, Evan E

    Bioinformatics (Oxford, England)

    2022  Volume 38, Issue 7, Page(s) 2049–2051

    Abstract: Summary: The visualization and analysis of genomic repeats is typically accomplished using dot plots; however, the emergence of telomere-to-telomere assemblies with multi-megabase repeats requires new visualization strategies. Here, we introduce ... ...

    Abstract Summary: The visualization and analysis of genomic repeats is typically accomplished using dot plots; however, the emergence of telomere-to-telomere assemblies with multi-megabase repeats requires new visualization strategies. Here, we introduce StainedGlass, which can generate publication-quality figures and interactive visualizations that depict the identity and orientation of multi-megabase tandem repeat structures at a genome-wide scale. The tool can rapidly reveal higher-order structures and improve the inference of evolutionary history for some of the most complex regions of genomes.
    Availability and implementation: StainedGlass is implemented using Snakemake and available open source under the MIT license at https://mrvollger.github.io/StainedGlass/.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Software ; Genomics ; Tandem Repeat Sequences ; Biological Evolution
    Language English
    Publishing date 2022-01-11
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btac018
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  9. Article ; Online: Long-read mapping to repetitive reference sequences using Winnowmap2.

    Jain, Chirag / Rhie, Arang / Hansen, Nancy F / Koren, Sergey / Phillippy, Adam M

    Nature methods

    2022  Volume 19, Issue 6, Page(s) 705–710

    Abstract: Approximately 5-10% of the human genome remains inaccessible due to the presence of repetitive sequences such as segmental duplications and tandem repeat arrays. We show that existing long-read mappers often yield incorrect alignments and variant calls ... ...

    Abstract Approximately 5-10% of the human genome remains inaccessible due to the presence of repetitive sequences such as segmental duplications and tandem repeat arrays. We show that existing long-read mappers often yield incorrect alignments and variant calls within long, near-identical repeats, as they remain vulnerable to allelic bias. In the presence of a nonreference allele within a repeat, a read sampled from that region could be mapped to an incorrect repeat copy. To address this limitation, we developed a new long-read mapping method, Winnowmap2, by using minimal confidently alignable substrings. Winnowmap2 computes each read mapping through a collection of confident subalignments. This approach is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats. Our experiments highlight that Winnowmap2 successfully addresses the issue of allelic bias, enabling more accurate downstream variant calls in repetitive sequences.
    MeSH term(s) Alleles ; Genome, Human ; Humans ; Repetitive Sequences, Nucleic Acid/genetics ; Segmental Duplications, Genomic ; Sequence Analysis, DNA ; Tandem Repeat Sequences
    Language English
    Publishing date 2022-04-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-022-01457-8
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  10. Article ; Online: Telomere-to-telomere assembly of diploid chromosomes with Verkko.

    Rautiainen, Mikko / Nurk, Sergey / Walenz, Brian P / Logsdon, Glennis A / Porubsky, David / Rhie, Arang / Eichler, Evan E / Phillippy, Adam M / Koren, Sergey

    Nature biotechnology

    2023  Volume 41, Issue 10, Page(s) 1474–1482

    Abstract: The Telomere-to-Telomere consortium recently assembled the first truly complete sequence of a human genome. To resolve the most complex repeats, this project relied on manual integration of ultra-long Oxford Nanopore sequencing reads with a high- ... ...

    Abstract The Telomere-to-Telomere consortium recently assembled the first truly complete sequence of a human genome. To resolve the most complex repeats, this project relied on manual integration of ultra-long Oxford Nanopore sequencing reads with a high-resolution assembly graph built from long, accurate PacBio high-fidelity reads. We have improved and automated this strategy in Verkko, an iterative, graph-based pipeline for assembling complete, diploid genomes. Verkko begins with a multiplex de Bruijn graph built from long, accurate reads and progressively simplifies this graph by integrating ultra-long reads and haplotype-specific markers. The result is a phased, diploid assembly of both haplotypes, with many chromosomes automatically assembled from telomere to telomere. Running Verkko on the HG002 human genome resulted in 20 of 46 diploid chromosomes assembled without gaps at 99.9997% accuracy. The complete assembly of diploid genomes is a critical step towards the construction of comprehensive pangenome databases and chromosome-scale comparative genomics.
    MeSH term(s) Humans ; Sequence Analysis, DNA/methods ; Diploidy ; Genomics/methods ; Genome, Human/genetics ; Telomere/genetics ; High-Throughput Nucleotide Sequencing/methods
    Language English
    Publishing date 2023-02-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1311932-1
    ISSN 1546-1696 ; 1087-0156
    ISSN (online) 1546-1696
    ISSN 1087-0156
    DOI 10.1038/s41587-023-01662-6
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