Searching journal content for articles similar to Rahman and Medvedev 32 (9): 1746.

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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...), as well as the refined correction of errors in long reads (Luo et al. 2022). For the latter, greatest improvements were observed for long reads stemming from metas. The favorable usage of variation graphs in the assembly of s from mixed samples (Baaijens et al. 2019, 2020) is an additional hint...
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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
...of population stratification.Measuring the effects of upstream noiseArtifacts of noise and errors in IBD estimation pipelines, including phasing switch errors, false-positive IBD segments, missing IBD segments, and incorrect IBD segment boundaries, negatively affect the quality of IBD estimation and...
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Method: Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs
- Juri Kuronen,
- Samuel T. Horsfield,
- Anna K. Pöntinen,
- Sudaraka Mallawaarachchi,
- Sergio Arredondo-Alonso,
- Harry Thorpe,
- Rebecca A. Gladstone,
- Rob J.L. Willems,
- Stephen D. Bentley,
- Nicholas J. Croucher,
- Johan Pensar,
- John A. Lees,
- Gerry Tonkin-Hill,
- and Jukka Corander
Genome Res. July 2024 34: 1081-1088; Published in Advance August 12, 2024, doi:10.1101/gr.278485.123
...representation of the variation present across a collection of assemblies that can be utilized for a wide range of applications, including GWAS (Jaillard et al. 2018; Lees et al. 2020) and genotyping (Iqbal et al. 2012). Within a colored cdBG, variable length sequences, or “unitigs,” represent loci within each...
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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...and scaffolding of Verkko's ULA assembly graph. Hi-C read pairs are first aligned to the assembled unitigs with BWA-MEM (Li 2013). All read pairs in which at least one read is mapped ambiguously (mapping quality of zero, typically multimappers from homozygous regions of different haplotypes) are ignored...
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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
...75080, USA Corresponding author: chirag@iisc.ac.inAbstractModern pan graphs are built using haplotype-resolved assemblies. When mapping reads to a pan graph, prioritizing alignments that are consistent with the known haplotypes improves genotyping accuracy. However, the existing rigorous formulations...
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Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
- Zepu Miao and
- Jia-Xing Yue
Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
...-level telomere-to-telomere (T2T) assemblies for diverse organisms, including humans (Yue et al. 2017; Jiao and Schneeberger 2020; Nurk et al. 2022). With such a T2T reference assembly panel continuously expanding at both the population and species level, researchers began to use pan graphs to better represent...
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Method: Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT
- Andrea Cracco and
- Alexandru I. Tomescu
Genome Res. July 2023 33: 1198-1207; Published in Advance May 30, 2023, doi:10.1101/gr.277615.122
...assembly graph (Drezen et al. 2014; Ruan and Li 2020). However, by replacing each unitig with, for example, an edge labeled with the label of the unitig (label obtained by identifying the overlapping (k − 2)-mers), one gets an equivalent graph, but of much smaller size. Such a graph is usually called...
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Method: Aligning distant sequences to graphs using long seed sketches
- Amir Joudaki,
- Alexandru Meterez,
- Harun Mustafa,
- Ragnar Groot Koerkamp,
- André Kahles,
- and Gunnar Rätsch
Genome Res. July 2023 33: 1208-1217; Published in Advance April 18, 2023, doi:10.1101/gr.277659.123
..., read error correction, and assembly. We propose a novel seeding approach that relies on long inexact matches rather than short exact matches, and show that it yields a better time-accuracy trade-off in settings with up to a mutation rate. We use sketches of a subset of graph nodes, which are more...
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RECOMB 2022 Special/Methods: Lossless indexing with counting de Bruijn graphs
- Mikhail Karasikov,
- Harun Mustafa,
- Gunnar Rätsch,
- and André Kahles
Genome Res. September 2022 32: 1754-1764; Published in Advance May 24, 2022, doi:10.1101/gr.276607.122
...with TCG-Aligner (see the Methods subsection “Trace-consistent graph-based aligner (TCG-Aligner)”) and other methods that support queries (BLAST, MegaBLAST, and PufferFish), we assembled a list of nine defining mutations of the SARS-CoV-2 21A (Delta) variant spike protein. This included six sequences...
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Research: Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements
- Luisa Berná,
- Pablo Marquez,
- Andrés Cabrera,
- Gonzalo Greif,
- María E. Francia,
- and Carlos Robello
Genome Res. May 2021 31: 823-833; Published in Advance April 27, 2021, doi:10.1101/gr.262832.120
...exist between species and strains. Our results correct assembly artifacts that are currently widely distributed in the database of N. caninum and T. gondii and, more importantly, highlight the mitochondria as a previously oversighted source of variability and pave the way for a change in the paradigm...

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