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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
.... 2020) based on individual k-mer catalogs generated with FastK (https://github.com/thegenemyers/FASTK, vApril 18 2021) and k-mer sizes 20, 30, and 40.Trimmed files were mapped with BWA-MEM v2.1 (Vasimuddin et al. 2019) against the best-assembled cichlid reference available at the time of this study...
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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
...approach (Andrews et al. 2023) is warranted.MethodsTE annotationThe TE library (ssal_repeats_v5.1) used to annotate TEs in this study is described in detail by Minkley (2018). To generate a TE annotation of the salmon (ICSASG v2 assembly), we used RepeatMasker version 4.1.2-p1 (Smit et al. 2015) under...
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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
..., and physiological genomics, illuminating processes such as environmental adaptation, species diversification, social behavior, or sex determination (Rittschof et al. 2014; Capel 2017; Salzburger 2018; Kim et al. 2019; Xie et al. 2019; Greenway et al. 2020). Around two hundred fish species have reference assemblies...
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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
...) technologies continue to make whole- sequencing more complete, affordable, and accurate. LRS provides significant advantages over short-read sequencing approaches, including phased de novo assembly, access to previously excluded genomic regions, and discovery of more complex structural variants (SVs...
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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
...–Coull binomial confidence interval.Although gold-standard data sets like HG002 are very useful for benchmarking, they have many limitations. Out of necessity, calls are only made in well-behaved regions of the , excluding structural variants in so-called “dark” areas of the where reads cannot be assembled...
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Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
- Ying Zhou,
- Li Song,
- and Heng Li
Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
...Full-resolution HLA and KIR gene annotations for human assemblies Ying Zhou1, Li Song2 and Heng Li1,3 1Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA; 2Department of Biomedical Data Science, Dartmouth College, Hanover, New Hampshire 03755, USA; 3...
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Resource: Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
- Bo Zhou,
- Steve S. Ho,
- Stephanie U. Greer,
- Xiaowei Zhu,
- John M. Bell,
- Joseph G. Arthur,
- Noah Spies,
- Xianglong Zhang,
- Seunggyu Byeon,
- Reenal Pattni,
- Noa Ben-Efraim,
- Michael S. Haney,
- Rajini R. Haraksingh,
- Giltae Song,
- Hanlee P. Ji,
- Dimitri Perrin,
- Wing H. Wong,
- Alexej Abyzov,
- and Alexander E. Urban
Genome Res. March 2019 29: 472-484; Published in Advance February 8, 2019, doi:10.1101/gr.234948.118
...and nonreference retrotransposon insertions. Many SVs were phased, assembled, and experimentally validated. We identified multiple allele-specific deletions and duplications within the tumor suppressor gene FHIT. Taking aneuploidy into account, we reanalyzed K562 RNA-seq and whole- bisulfite sequencing data...
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Resource: Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
- Rei Kajitani,
- Kouta Toshimoto,
- Hideki Noguchi,
- Atsushi Toyoda,
- Yoshitoshi Ogura,
- Miki Okuno,
- Mitsuru Yabana,
- Masayuki Harada,
- Eiji Nagayasu,
- Haruhiko Maruyama,
- Yuji Kohara,
- Asao Fujiyama,
- Tetsuya Hayashi,
- and Takehiko Itoh
Genome Res. August 2014 24: 1384-1395; Published in Advance April 22, 2014, doi:10.1101/gr.170720.113
...Resource Efficient de novo assembly of highly heterozygous s from whole- shotgun short reads Rei Kajitani,1 Kouta Toshimoto,1,2 Hideki Noguchi,3 Atsushi Toyoda,3,4 Yoshitoshi Ogura,5,6 Miki Okuno,1 Mitsuru Yabana,1 Masayuki Harada,1 Eiji Nagayasu,7 Haruhiko Maruyama,7 Yuji Kohara,8 Asao Fujiyama,3...
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Resource: Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
- Jonathan M. Mudge,
- Irwin Jungreis,
- Toby Hunt,
- Jose Manuel Gonzalez,
- James C. Wright,
- Mike Kay,
- Claire Davidson,
- Stephen Fitzgerald,
- Ruth Seal,
- Susan Tweedie,
- Liang He,
- Robert M. Waterhouse,
- Yue Li,
- Elspeth Bruford,
- Jyoti S. Choudhary,
- Adam Frankish,
- and Manolis Kellis
Genome Res. December 2019 29: 2073-2087; Published in Advance September 19, 2019, doi:10.1101/gr.246462.118
...of the hg38/GRCh38 human reference assembly in each of the six reading frames using alignments of 29 mammalian s. Each codon gets a positive score if the alignment of that codon is more likely to have arisen under a model of protein-coding evolution than under a model of noncoding evolution. Because...
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