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Research: Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T
- Luis F. Paulin,
- Jeremy Fan,
- Kieran O'Neill,
- Erin Pleasance,
- Vanessa L. Porter,
- Steven J.M. Jones,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 621-631; Published in Advance March 17, 2025, doi:10.1101/gr.279352.124
.... 2024). We utilized four independent COLO829/COLO829BL samples from four sequencing centers profiled using the Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) long-read platforms, including the reads from the most recently established benchmark (Supplemental Table 1; Espejo Valle...
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Method: Benchmarking bulk and single-cell variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries
- Matthew Wiens,
- Hossein Farahani,
- R. Wilder Scott,
- T. Michael Underhill,
- and Ali Bashashati
Genome Res. August 2024 34: 1196-1210; Published in Advance August 15, 2024, doi:10.1101/gr.277066.122
...et al. 2019; Zhou et al. 2020; Lu et al. 2021). An additional benefit is that modality-specific sequence-altering effects such as RNA editing can be investigated at the single-cell level (Picardi et al. 2017).The most popular single-cell methodology is the Chromium platform provided by 10x Genomics...
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Method: Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics
- David C. Danko,
- Dmitry Meleshko,
- Daniela Bezdan,
- Christopher Mason,
- and Iman Hajirasouliha
Genome Res. January 2019 29: 116-124; Published in Advance December 6, 2018, doi:10.1101/gr.235499.118
....7171/jbt.17-2801-006 ↵McIntyre ABR, Ounit R, Afshinnekoo E, Prill RJ, Hénaff E, Alexander N, Minot SS, Danko D, Foox J, Ahsanuddin S, et al. 2017. Comprehensive benchmarking and ensemble approaches for metagenomic classifiers. Genome Biol 18: 182. doi:10.1186/s13059-017-1299-7 ↵Orenstein Y, Pellow D...
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Research: Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules
- Jonathon L. Baker,
- James T. Morton,
- Márcia Dinis,
- Ruth Alvarez,
- Nini C. Tran,
- Rob Knight,
- and Anna Edlund
Genome Res. January 2021 31: 64-74; Published in Advance November 25, 2020, doi:10.1101/gr.265645.120
.... De novo assembly of metagenomic sequencing obtained 527 meta-assembled s (MAGs), representing 150 bacterial species. Forty-two of these species had no s in public repositories, thereby representing novel taxa. These new s greatly expanded the known pans of many oral clades, including the enigmatic...
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Resource: Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform
- Liubomir Chorbadjiev,
- Murat Cokol,
- Zohar Weinstein,
- Kevin Shi,
- Christopher Fleisch,
- Nikolay Dimitrov,
- Svetlin Mladenov,
- Ivo Todorov,
- Iordan Ivanov,
- Simon Xu,
- Steven Ford,
- Yoon-ha Lee,
- Boris Yamrom,
- Steven Marks,
- Adriana Munoz,
- Alex Lash,
- Natalia Volfovsky,
- and Ivan Iossifov
Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
...made it possible to pursue the search for variants associated with complex diseases. However, managing these large-scale data sets requires specialized computational tools to organize and analyze the extensive data. Genotypes and Phenotypes in Families (GPF) is an open-source platform that manages...
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Method: Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns
- Alla Mikheenko,
- Andrey D. Prjibelski,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. April 2022 32: 726-737; Published in Advance March 17, 2022, doi:10.1101/gr.276405.121
...molecule. Here, we present a novel platform-comparison method that combines barcoding strategies and long-read sequencing to sequence cDNA copies representing an individual RNA molecule on both Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). We compare these long-read pairs in terms...
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Method: Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics
- Alexey Vorobev,
- Marion Dupouy,
- Quentin Carradec,
- Tom O. Delmont,
- Anita Annamalé,
- Patrick Wincker,
- and Eric Pelletier
Genome Res. April 2020 30: 647-659; Published in Advance March 23, 2020, doi:10.1101/gr.253070.119
..., France Corresponding authors: voralexey@gmail.com, eric.pelletier@genoscope.cns.frAbstractLarge-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large...
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Resource: Benchmarking small-variant genotyping in polyploids
- Daniel P. Cooke,
- David C. Wedge,
- and Gerton Lunter
Genome Res. February 2022 32: 403-408; Published in Advance December 29, 2021, doi:10.1101/gr.275579.121
...are confidently determined with comprehensive benchmarks, polyploids have been neglected; there are no benchmarks measuring genotyping error rates for small variants using real sequencing reads. We previously introduced a variant calling method, Octopus, that accurately calls germline variants in diploids...
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Resource: Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants
- Michael N. Edmonson,
- Aman N. Patel,
- Dale J. Hedges,
- Zhaoming Wang,
- Evadnie Rampersaud,
- Chimene A. Kesserwan,
- Xin Zhou,
- Yanling Liu,
- Scott Newman,
- Michael C. Rusch,
- Clay L. McLeod,
- Mark R. Wilkinson,
- Stephen V. Rice,
- Thierry Soussi,
- J. Paul Taylor,
- Michael Benatar,
- Jared B. Becksfort,
- Kim E. Nichols,
- Leslie L. Robison,
- James R. Downing,
- and Jinghui Zhang
Genome Res. September 2019 29: 1555-1565; Published in Advance August 22, 2019, doi:10.1101/gr.250357.119
...pathogenicity following the American College of Medical Genetics and Genomics (ACMG) guidelines (Richards et al. 2015) have also been developed (Patel et al. 2017). Although each resource offers valuable information to help researchers classify variant pathogenicity, integrated platforms are needed to provide...
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Resource: A platform for curated products from novel open reading frames prompts reinterpretation of disease variants
- Matthew D.C. Neville,
- Robin Kohze,
- Chaitanya Erady,
- Narendra Meena,
- Matthew Hayden,
- David N. Cooper,
- Matthew Mort,
- and Sudhakaran Prabakaran
Genome Res. February 2021 31: 327-336; Published in Advance January 19, 2021, doi:10.1101/gr.263202.120
...for functional importance, and show the potential implications for functional interpretation of genetic variants in nORFs. Our results indicate that some variants that were previously classified as being benign or of uncertain significance may have to be reinterpreted.Recent evidence from proteomics...

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