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Review: k-mer approaches for biodiversity genomics
- Katharine M. Jenike,
- Lucía Campos-Domínguez,
- Marilou Boddé,
- José Cerca,
- Christina N. Hodson,
- Michael C. Schatz,
- and Kamil S. Jaron
Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
...), and minimap2 (Li 2018) and practically all assemblers (for a review, see Li and Durbin 2024). More recently, k-mers have emerged as a popular framework for analyzing genomic data sets directly in methods such as profiling, thanks to the development of user-friendly tools such as GenomeScope (Vurture et al...
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Method: Memory-bound k-mer selection for large and evolutionarily diverse reference libraries
- Ali Osman Berk Şapcı and
- Siavash Mirarab
Genome Res. September 2024 34: 1455-1467; Published in Advance August 29, 2024, doi:10.1101/gr.279339.124
...minimizers and finding taxon-specific k-mers. However, we contend that these strategies are inadequate, especially when reference sets are taxonomically imbalanced, as are most microbial libraries. In this paper, we explore approaches for selecting a fixed-size subset of k-mers present in an ultra-large data...
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Method: k-mer manifold approximation and projection for visualizing DNA sequences
- Chengbo Fu,
- Einari A. Niskanen,
- Gong-Hong Wei,
- Zhirong Yang,
- Marta Sanvicente-García,
- Marc Güell,
- and Lu Cheng
Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
...and reveal conserved regions. Although these approaches focus on k-mer similarities, they do not address the structure of the k-mer manifold, which could offer deeper insights into relationships among k-mers and further enhance motif discovery.To extract the biological information from DNA sequences...
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Method: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
- Romain Derelle,
- Johanna von Wachsmann,
- Tommi Mäklin,
- Joel Hellewell,
- Timothy Russell,
- Ajit Lalvani,
- Leonid Chindelevitch,
- Nicholas J. Croucher,
- Simon R. Harris,
- and John A. Lees
Genome Res. October 2024 34: 1661-1673; Published in Advance October 15, 2024, doi:10.1101/gr.279449.124
...in ska align, which can be usefully retained by ska map.We repeated the SKA2 analyses to assess the impact of split k-mer size on its SNP detection. Using k-mer sizes ranging from 21 to 61 nucleotides, in increments of 10, we observed similar numbers of identified SNPs between k = 21 and k = 51 for S...
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Method: Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases
- Ming Yan,
- Thea O. Andersen,
- Phillip B. Pope,
- and Zhongtang Yu
Genome Res. February 2025 35: 368-378; Published in Advance December 27, 2024, doi:10.1101/gr.279825.124
...analyses of protozoa and fungi within more than 1000 rumen metas, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi...
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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
...-recall curve.To assess the strain-level performance of sylph, a recent excellent species-level meta profiling tool, we ran it on the sim-low and sim-high data sets. Sylph generally exhibits substantially lower recall than other tools (Supplemental Fig. S1), likely because its k-mer reassignment strategy lacks...
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Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
- Rashid Al-Abri and
- Gamze Gürsoy
Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
...for these loci (Supplemental Table S1). We simulated the samples with 30× coverage and a sequencing error profile based on the Illumina HiSeq X platform (see Methods). We simulated homozygous and heterozygous expansions in 30 TR loci with copy numbers ranging from 200 to 1000 for a total of 540 samples. We...
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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...enriched for promoter signatures. Thus, our results highlight the importance of maintaining the ratio of antibody to cell number as constant as possible, in particular in chromatin profiling experiments aimed at studying the impact of perturbations (e.g., by small molecules or CRISPRi) to allow proper...
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Research: Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants
- Juan Deng,
- Ya-Jing Liu,
- Wen-Tian Wei,
- Qi-Xuan Huang,
- Li-Ping Zhao,
- Ling-Yun Luo,
- Qi Zhu,
- Lin Zhang,
- Yuan Chen,
- Yan-Ling Ren,
- Shan-Gang Jia,
- Yu-Luan Lin,
- Ji Yang,
- Feng-Hua Lv,
- Hong-Ping Zhang,
- Feng-E Li,
- Li Li,
- and Meng-Hua Li
Genome Res. October 2023 33: 1690-1707; Published in Advance October 26, 2023, doi:10.1101/gr.278239.123
...Single-cell transcriptome and meta profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants Juan Deng1,2,7, Ya-Jing Liu1,7, Wen-Tian Wei1, Qi-Xuan Huang1, Li-Ping Zhao3,4, Ling-Yun Luo1, Qi Zhu2, Lin Zhang2, Yuan Chen2, Yan-Ling Ren5, Shan-Gang Jia6...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...1 Title 1 Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals 2 conserved gene alterations linked to Parkinson’s disease 3 Running title: Substantia nigra aging linked to Parkinson 4 Kangli Wang1, Weikun Xia1, Yingli Gu1, Songpeng Zu1, Qian Yang2, Maria Luisa Amaral1...
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