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Resource: Whole-genome sequencing of diverse 351 cultured prokaryotes including as-yet-unsequenced type strains
- Shingo Kato,
- Sachiko Masuda,
- Arisa Shibata,
- Takashi Itoh,
- Mitsuo Sakamoto,
- Ken Shirasu,
- and Moriya Ohkuma
Genome Res. April 2026 36: 875-884; Published in Advance April 7, 2026, doi:10.1101/gr.281026.125
...from isolated strains publicly available from culture collections, -driven hypotheses from our analyses can be verified by cultivation experiments with the isolates.Contamination-level assessmentAlthough some s showed high values of contamination level, many of these s were completed. For instance...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...-seq reads and bias in the peak calling is a potential issue. We therefore assessed the level of multimapped ATAC-seq reads in TEs versus other genomic regions for one of the brain samples. This analysis showed that -wide multimapping levels were 14%, whereas reads mapping to TEs from larger subfamilies...
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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
...(Supplemental Fig. S4).Based on this depth distribution and previous recommendations (the data set of Carson et al. [2014] favored a DP of eight), we assessed the impact of different depth filters on patterns and values of retained heterozygosity. We did so under the assumption that variants with unusually high...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...for variant discovery: read-based and assembly-based methods. We define read-based methodologies as those requiring alignment of individual sequencing reads to a reference and applying specific read-based variant-calling algorithms to these alignments to identify variants. Assembly-based methods, in contrast...
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Method: Accurate short-read alignment through r-index-based pangenome indexing
- Rahul Varki,
- Massimiliano Rossi,
- Eddie Ferro,
- Marco Oliva,
- Erik Garrison,
- Ben Langmead,
- and Christina Boucher
Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
..., running Red Hat Enterprise Linux 8.8. The compiler used was g++ version 9.3.0. The time and memory values reported were obtained from the Snakemake benchmark files.Alignment to MHC panMoni-align balanced indexing speed and memory efficiency, delivering moderate yet competitive performance compared with vg...
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Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
- Shuangxi Ji,
- Tong Zhu,
- Ankit Sethia,
- and Wenyi Wang
Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
...as a major contributing caller to reach final consensus calls by The Cancer Genome Atlas (TCGA) PanCanAtlas project (Ellrott et al. 2018), across approximately 13,000 tumor samples, and the International Cancer Genome Consortium Pan-Cancer Analysis of Whole Genomes (ICGC-PCAWG) initiative (The ICGC/TCGA Pan...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
...is equally supported by the sequence alignment. These 26,692 WGD-aware teleost gene trees predict that the ancestral of teleost fish contained 46,206 genes after the duplication event, in line with the latest estimates from the Ensembl database (49,255 ancestral teleost genes in release v100; Methods).A high...
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Method: scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment
- Zhitao Huang,
- Ruiqing Zheng,
- Pengzhen Jia,
- Xuhua Yan,
- Jinmiao Chen,
- and Min Li
Genome Res. February 2026 36: 387-396; Published in Advance January 20, 2026, doi:10.1101/gr.280410.125
...experimentTo assess the robustness of scSHEFT under different hyperparameter settings, we conducted a systematic sensitivity analysis using four data sets, each containing more than 5000 cells (Supplemental Fig. S6). We focused on the main loss weights: anchor inter alignment (α1, anchor loss), center inter...
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Method: Fast sequence alignment for centromeres with RaMA
- Pinglu Zhang,
- Yanming Wei,
- Qinzhong Tian,
- Quan Zou,
- and Yansu Wang
Genome Res. May 2025 35: 1209-1218; Published in Advance February 12, 2025, doi:10.1101/gr.279763.124
...are presented in Supplemental Tables S1 and S2, providing a comprehensive comparison of the capabilities of these alignment tools.We defined two categories of reliable regions based on sequence identity and rare matches. For identity assessment based on previous work (Logsdon et al. 2024), the reference...
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Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
...or aligned well. Deletions in these regions may still be highly relevant to disease (Ebbert et al. 2019) but are not evaluated when using gold-standard benchmarks. Furthermore, because of the small number of gold-standard structural variant data sets, callers may overfit to a handful of data sets, making...

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