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Method: Accurate and fast graph-based pangenome annotation and clustering with ggCaller
- Samuel T. Horsfield,
- Gerry Tonkin-Hill,
- Nicholas J. Croucher,
- and John A. Lees
Genome Res. September 2023 33: 1622-1637; Published in Advance August 24, 2023, doi:10.1101/gr.277733.123
...alignment and annotations between s can make results difficult to interpret. Consequently, the correct interpretation of macrolide resistance PGWAS in this species has proven challenging using previous approaches (Lees et al. 2016). To highlight issues with using linear references for annotation, unitigs...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...sequence difference, with 0.1%–0.25% pairwise divergence between Lake Malawi species. These were based on aligning short reads to a single linear reference and ignored the contribution of larger-scale structural variants (SVs). We constructed a pan graph that integrates six new and two existing long...
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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
..., and other repetitive elements, leading to misleading alignments of short and long reads when using a linear reference. We align 250 short-read sequencing samples spanning 15 cattle breeds to the pan graph, further validating that the alleles of the SV segregate with head depigmentation. We estimate...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 2023 33: 463-477; Published in Advance April 3, 2023, doi:10.1101/gr.277372.12
...of the sheep . On the other hand, our pan analysis is based on the reference . With the gradual improvement of the pan model (Liao et al. 2022; Wang et al. 2022b), a graph-based sheep pan reference will eventually be available.Despite advances and application of third-generation sequencing technologies...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 27, 2023 ; Published in Advance March 27, 2023, doi:10.1101/gr.277372.122
...in pan-based inference have largely addressed previous challenges in the discovery of diverse SV types including multiallelic complex variations (Crysnanto et al. 2021; Leonard et al. 2022). By integrating SVs and reference , the pan graph approach can particularly improve SV genotyping accuracy of short...
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Method: Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
- Byron J. Smith,
- Chunyu Zhao,
- Veronika Dubinkina,
- Xiaofan Jin,
- Liron Zahavi,
- Saar Shoer,
- Jacqueline Moltzau-Anderson,
- Eran Segal,
- and Katherine S. Pollard
Genome Res. May 2025 35: 1247-1260; Published in Advance April 10, 2025, doi:10.1101/gr.279543.124
...changes to the pan reference database construction procedure and the pan profiling method. Together, these updates clean, functionally annotate, and expand the phylogenetic coverage of MIDAS pan profiling, providing a foundation for accurately estimating and interpreting gene content across species. MIDAS...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...in the GRCh37 reference —78% of which contained extensive degenerate short TRs, particularly in (G + C)-rich areas. They also resolved over 26,000 structural variants at base pair resolution, including previously undetectable inversions, complex insertions, and long TR tracts. This landmark study highlighted...
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Resource: Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)
- Sanjida H. Rangwala,
- Anatoliy Kuznetsov,
- Victor Ananiev,
- Andrea Asztalos,
- Evgeny Borodin,
- Vladislav Evgeniev,
- Victor Joukov,
- Vadim Lotov,
- Ravinder Pannu,
- Dmitry Rudnev,
- Andrew Shkeda,
- Eric M. Weitz,
- and Valerie A. Schneider
Genome Res. January 2021 31: 159-169; Published in Advance November 25, 2020, doi:10.1101/gr.266932.120
...sequence viewers supporting linear sequence representations can display alignments of genomic or protein sequence in parallel with annotated features and experimental data rendered in the form of boxes, line graphs...
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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
...variants are characterized, some functional interpretation by using the annotation of the reference, a well-defined coordinate system, computational scalability that can be trivially parallelized, and flexibility as new samples can be added to an already processed data set.For some purposes, ordering...
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Method: Accurate reconstruction of bacterial pan- and core genomes with PEPPAN
- Zhemin Zhou,
- Jane Charlesworth,
- and Mark Achtman
Genome Res. November 2020 30: 1667-1679; Published in Advance October 14, 2020, doi:10.1101/gr.260828.120
...are gained or lost multiple times. This generates complex patterns of presence/absence along the phylogeny. Therefore, including paralogous genes in a phylogenetic analysis may lead to inaccurate interpretations. State-of-the-art pan pipelines implement either graph- or tree-based algorithms...
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