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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...: chirag@iisc.ac.inAbstractAffordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single-nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference is unreliable in highly polymorphic...
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Method: Haplotype-aware sequence alignment to pangenome graphs
- Ghanshyam Chandra,
- Daniel Gibney,
- and Chirag Jain
Genome Res. September 2024 34: 1265-1275; Published in Advance July 16, 2024, doi:10.1101/gr.279143.124
...in Minichain (v1.3). Our experiments show that the algorithm produces alignment with fewer false recombinations and better selection of the correct haplotypes.More work is needed, especially to establish that the proposed haplotype-aware mapping algorithms can lead to improvements in routine genomic...
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Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...of the top-performing methods will depend upon the feasibility of whole- alignment, availability of RNA-seq data, importance of capturing noncoding parts of the transcriptome, and, when whole- alignment is not feasible, the relative performance in BUSCO recovery between BRAKER3 and StringTie. When whole...
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Research: Gaps and complex structurally variant loci in phased genome assemblies
- David Porubsky,
- Mitchell R. Vollger,
- William T. Harvey,
- Allison N. Rozanski,
- Peter Ebert,
- Glenn Hickey,
- Patrick Hasenfeld,
- Ashley D. Sanders,
- Catherine Stober,
- Human Pangenome Reference Consortium,
- Jan O. Korbel,
- Benedict Paten,
- Tobias Marschall,
- and Evan E. Eichler
Genome Res. April 2023 33: 496-510; Published in Advance May 10, 2023, doi:10.1101/gr.277334.122
...) and the Human Pan Reference Consortium (HPRC) (Ebert et al. 2021; Liao et al. 2023). Efforts such as these have generated data with different sequence technologies and applied different algorithms and strategies to generate multiple phased human s, including some that now rival the contiguity and accuracy...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...of individual Hydra promoter regions (Supplemental Fig. S7; Vogg et al. 2019), supporting the accuracy of our -wide approach. We then used our whole- alignment to classify genomic features as either conserved or nonconserved (for details, see Supplemental Material). We provide lists of conserved noncoding...
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Resource: Alignathon: a competitive assessment of whole-genome alignment methods
- Dent Earl,
- Ngan Nguyen,
- Glenn Hickey,
- Robert S. Harris,
- Stephen Fitzgerald,
- Kathryn Beal,
- Igor Seledtsov,
- Vladimir Molodtsov,
- Brian J. Raney,
- Hiram Clawson,
- Jaebum Kim,
- Carsten Kemena,
- Jia-Ming Chang,
- Ionas Erb,
- Alexander Poliakov,
- Minmei Hou,
- Javier Herrero,
- William James Kent,
- Victor Solovyev,
- Aaron E. Darling,
- Jian Ma,
- Cedric Notredame,
- Michael Brudno,
- Inna Dubchak,
- David Haussler,
- and Benedict Paten
Genome Res. December 2014 24: 2077-2089; Published in Advance October 1, 2014, doi:10.1101/gr.174920.114
...), which was used to realignMULTIZ based alignments in this competition but can in principle refine alignments from any multiple alignment tool. We also tested pairwise WGAs from the GenomeMatch team. As might be expected, not all algorithms/ pipelines were run for all test sets. Participants cited...
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Method: Chromosome assembly of large and complex genomes using multiple references
- Mikhail Kolmogorov,
- Joel Armstrong,
- Brian J. Raney,
- Ian Streeter,
- Matthew Dunn,
- Fengtang Yang,
- Duncan Odom,
- Paul Flicek,
- Thomas M. Keane,
- David Thybert,
- Benedict Paten,
- and Son Pham
Genome Res. November 2018 28: 1720-1732; Published in Advance October 19, 2018, doi:10.1101/gr.236273.118
.... First, we present a new algorithm for synteny block reconstruction for multiple mammalian s. Our approach combines Cactus, a multiple whole- aligner (Paten et al. 2011), with a new iterative graph simplification algorithm that produces hierarchical synteny blocks on multiple scales. Second, we show how...
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Review: Genome graphs and the evolution of genome inference
- Benedict Paten,
- Adam M. Novak,
- Jordan M. Eizenga,
- and Erik Garrison
Genome Res. May 2017 27: 665-676; Published in Advance March 30, 2017, doi:10.1101/gr.214155.116
...graphs—has proven to be a challenge, and the tools in Table 2 have approached these problems in various ways. Local alignment Although extending fully ordered dynamic programming algorithms to partially ordered directed acyclic graphs is relatively simple (Lee et al. 2002), sequence graphs...
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Method: Predicting transfer RNA gene activity from sequence and genome context
- Bryan P. Thornlow,
- Joel Armstrong,
- Andrew D. Holmes,
- Jonathan M. Howard,
- Russell B. Corbett-Detig,
- and Todd M. Lowe
Genome Res. January 2020 30: 85-94; Published in Advance December 19, 2019, doi:10.1101/gr.256164.119
...a Cactus graph (Paten et al. 2011a,b; Nguyen et al. 2015; Armstrong et al. 2019), which is a reference-free whole- alignment. Usage of a Cactus graph enhances detection of synteny and facilitates extraction of alignments for specific regions in multiple s. The Cactus graph used in this study includes 29...
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Research: Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
- Todd P. Michael,
- Evan Ernst,
- Nolan Hartwick,
- Philomena Chu,
- Douglas Bryant,
- Sarah Gilbert,
- Stefan Ortleb,
- Erin L. Baggs,
- K. Sowjanya Sree,
- Klaus J. Appenroth,
- Joerg Fuchs,
- Florian Jupe,
- Justin P. Sandoval,
- Ksenia V. Krasileva,
- Ljudmylla Borisjuk,
- Todd C. Mockler,
- Joseph R. Ecker,
- Robert A. Martienssen,
- and Eric Lam
Genome Res. February 2021 31: 225-238; Published in Advance December 23, 2020, doi:10.1101/gr.266429.120
..., 2008; Hoff et al. 2016, 2019). A second set of predictions was produced by generating a whole- multiple sequence alignment of all duckweed species with Cactus (Paten et al. 2011) and running AUGUSTUS in CGP mode (König et al. 2016). The final set of predictions was produced by running AUGUSTUS within...
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