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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
...Strain-level metagenomic profiling using pan graphs with PanTax Wenhai Zhang1,2,5, Yuansheng Liu3,5, Guangyi Li2,5, Jialu Xu2, Enlian Chen2, Alexander Schönhuth4 and Xiao Luo1,2 1Hunan Research Center of the Basic Discipline for Cell Signaling, Hunan University, Changsha, Hunan 410082, China; 2...
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Method: Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters
- Jens-Uwe Ulrich and
- Bernhard Y. Renard
Genome Res. June 2024 34: 914-924; Published in Advance June 17, 2024, doi:10.1101/gr.278623.123
..., 15745 Wildau, Germany; 3Department of Mathematics and Computer Science, Free University of Berlin, 14195 Berlin, Germany Corresponding authors: jens-uwe.ulrich@hpi.de, bernhard.renard@hpi.deAbstractMetagenomic long-read sequencing is gaining popularity for various applications, including pathogen...
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Resource: Windshield splatter analysis with the Galaxy metagenomic pipeline
- Sergei Kosakovsky Pond,
- Samir Wadhawan,
- Francesca Chiaromonte,
- Guruprasad Ananda,
- Wen-Yu Chung,
- James Taylor,
- Anton Nekrutenko,
- and The Galaxy Team
Genome Res. November 2009 19: 2144-2153; Published in Advance October 9, 2009, doi:10.1101/gr.094508.109
...such as CAMERA (Seshadri et al. 2007) or MG-RAST (Meyer et al. 2008) provide a powerful computational infrastructure, and visualization tools such as MEGAN (Huson et al. 2007) allow researchers to analyze the phylogenetic makeup of their metagenomic samples, metagenomic studies remain quite challenging. Indeed...
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Method: Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
- Yuhong Sun,
- Zhanwen Cheng,
- Xiang Li,
- Qing Yang,
- Bixi Zhao,
- Ziqi Wu,
- and Yu Xia
Genome Res. April 2023 33: 612-621; Published in Advance April 11, 2023, doi:10.1101/gr.277266.122
.... doi:10.1371/journal.pcbi.1004957 ↵Huson DH, Albrecht B, Bağcı C, Bessarab I, Górska A, Jolic D, Williams RB. 2018. MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs. Biol Direct 13: 6. doi:10.1186/s13062-018-0208-7 ↵Jousset A...
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Research: Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region
- Matthew T. Maurano,
- Sitharam Ramaswami,
- Paul Zappile,
- Dacia Dimartino,
- Ludovic Boytard,
- André M. Ribeiro-dos-Santos,
- Nicholas A. Vulpescu,
- Gael Westby,
- Guomiao Shen,
- Xiaojun Feng,
- Megan S. Hogan,
- Manon Ragonnet-Cronin,
- Lily Geidelberg,
- Christian Marier,
- Peter Meyn,
- Yutong Zhang,
- John Cadley,
- Raquel Ordoñez,
- Raven Luther,
- Emily Huang,
- Emily Guzman,
- Carolina Arguelles-Grande,
- Kimon V. Argyropoulos,
- Margaret Black,
- Antonio Serrano,
- Melissa E. Call,
- Min Jae Kim,
- Brendan Belovarac,
- Tatyana Gindin,
- Andrew Lytle,
- Jared Pinnell,
- Theodore Vougiouklakis,
- John Chen,
- Lawrence H. Lin,
- Amy Rapkiewicz,
- Vanessa Raabe,
- Marie I. Samanovic,
- George Jour,
- Iman Osman,
- Maria Aguero-Rosenfeld,
- Mark J. Mulligan,
- Erik M. Volz,
- Paolo Cotzia,
- Matija Snuderl,
- and Adriana Heguy
Genome Res. December 2020 30: 1781-1788; Published in Advance October 22, 2020, doi:10.1101/gr.266676.120
...Matthew T. Maurano1,2, Sitharam Ramaswami3, Paul Zappile3, Dacia Dimartino3, Ludovic Boytard4, André M. Ribeiro-dos-Santos1,2, Nicholas A. Vulpescu1,2, Gael Westby3, Guomiao Shen2, Xiaojun Feng2, Megan S. Hogan1,2, Manon Ragonnet-Cronin5, Lily Geidelberg5, Christian Marier3, Peter Meyn3, Yutong...
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Method: taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time
- André Corvelo,
- Wayne E. Clarke,
- Nicolas Robine,
- and Michael C. Zody
Genome Res. May 2018 28: 751-758; Published in Advance March 27, 2018, doi:10.1101/gr.225276.117
..., Auch AF, Qi J, Schuster SC. 2007. MEGAN analysis of metagenomic data. Genome Res 17: 377–386. ↵Kim D, Song L, Breitwieser FP, Salzberg SL. 2016. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res 26: 1721–1729. ↵Leinonen R, Sugawara H, Shumway M, International...
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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
...and specific cell types (Cheng et al. 2019). Rumen epithelial single-cell atlases of cattle and sheep obtained with scRNA-seq have been reported (Gao et al. 2021; Wu et al. 2022; Xue et al. 2022; Yuan et al. 2022). However, a comprehensive developmental cell atlas and a metagenomic characteristic map...
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Resource: Integrative analysis of environmental sequences using MEGAN4
- Daniel H. Huson,
- Suparna Mitra,
- Hans-Joachim Ruscheweyh,
- Nico Weber,
- and Stephan C. Schuster
Genome Res. September 2011 21: 1552-1560; Published in Advance June 20, 2011, doi:10.1101/gr.120618.111
..., addressing both the taxonomic and functional aspects. To facilitate such analyses, we have substantially extended MEGAN, a widely used taxonomic analysis program. The new program, MEGAN4, provides an integrated approach to the taxonomic and functional analysis of metagenomic, metatranscriptomic...
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Method: Pathoscope: Species identification and strain attribution with unassembled sequencing data
- Owen E. Francis,
- Matthew Bendall,
- Solaiappan Manimaran,
- Changjin Hong,
- Nathan L. Clement,
- Eduardo Castro-Nallar,
- Quinn Snell,
- G. Bruce Schaalje,
- Mark J. Clement,
- Keith A. Crandall,
- and W. Evan Johnson
Genome Res. October 2013 23: 1721-1729; Published in Advance July 10, 2013, doi:10.1101/gr.150151.112
...for applications in pathology, bioforensics, and biosurveillance. Given a particular clinical or metagenomic sample, our goal is to identify the specific species, strains, or substrains present in the sample, as well as accurately estimate the proportions of DNA originating from each source in the sample. Current...
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Next-Generation DNA Sequencing/Review: Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
- Micah Hamady and
- Rob Knight
Genome Res. July 2009 19: 1141-1152; Published in Advance April 21, 2009, doi:10.1101/gr.085464.108
...(for eukaryotes) are used as stable phylogenetic markers to define which lineages are present in a sample (Pace 1997), and metagenomic studies, in which community DNA is subject to shotgun sequencing (Rondon et al. 2000). Small subunit rRNA-based studies are sometimes also considered...

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