Searching journal content for articles similar to Fedarko et al. 32 (11-12): 2119.

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Review: Accurate and complete genomes from metagenomes
- Lin-Xing Chen,
- Karthik Anantharaman,
- Alon Shaiber,
- A. Murat Eren,
- and Jillian F. Banfield
Genome Res. March 2020 30: 315-333; Published in Advance March 18, 2020, doi:10.1101/gr.258640.119
...in metagenomic studiesAssembly of short metagenomic reads into contiguous segments of DNA is a computationally intensive task, and its effectiveness often depends on the complexity of the environment (Sharon and Banfield 2013). However, assembly of contigs/scaffolds offers many advantages over short-read...
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Method: Fast and accurate mapping of long reads to complete genome assemblies with VerityMap
- Andrey V. Bzikadze,
- Alla Mikheenko,
- and Pavel A. Pevzner
Genome Res. November/December 2022 32: 2107-2118; Published in Advance November 15, 2022, doi:10.1101/gr.276871.122
...genomics” (Nurk et al. 2020, 2022; Cheng et al. 2021) and “complete metagenomics” (Bickhart et al. 2022) is shifting the focus of read mapping from detecting mutations to detecting errors in the newly generated assemblies (see Supplemental Note 1, “Similarities and differences between detecting mutations...
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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
...-free and reference-based mapping to quickly and accurately genotype populations of bacteria using sequencing reads or assemblies. SKA2 is highly accurate for closely related samples, and in outbreak simulations, we show superior variant recall compared with reference-based methods, with no false positives. SKA2 can...
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Method: Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors
- Mara Lohde,
- Gabriel E. Wagner,
- Johanna Dabernig-Heinz,
- Adrian Viehweger,
- Sascha D. Braun,
- Stefan Monecke,
- Celia Diezel,
- Claudia Stein,
- Mike Marquet,
- Ralf Ehricht,
- Mathias W. Pletz,
- and Christian Brandt
Genome Res. November 2024 34: 2039-2047; Published in Advance October 23, 2024, doi:10.1101/gr.278848.123
...the effectiveness of Oxford Nanopore Technologies for accurate outbreak tracing by resequencing 33 isolates of a 3-year-long Klebsiella pneumoniae outbreak with Illumina short-read sequencing data as the point of reference. We detect considerable base errors through cgMLST and phylogenetic analysis of s sequenced...
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Method: Accurate sequencing of DNA motifs able to form alternative (non-B) structures
- Matthias H. Weissensteiner,
- Marzia A. Cremona,
- Wilfried M. Guiblet,
- Nicholas Stoler,
- Robert S. Harris,
- Monika Cechova,
- Kristin A. Eckert,
- Francesca Chiaromonte,
- Yi-Fei Huang,
- and Kateryna D. Makova
Genome Res. July 11, 2023 ; Published in Advance July 11, 2023, doi:10.1101/gr.277490.122
...of polymerases and helicases. Because sequencing technologies use these enzymes, theymight possess increased errors at non-B structures. To evaluate this, we analyzed error rates, read depth, and base quality of Illumina, Pacific Biosciences (PacBio) HiFi, and Oxford Nanopore Technologies (ONT) sequencing at non...
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Method: Microbial strain-level population structure and genetic diversity from metagenomes
- Duy Tin Truong,
- Adrian Tett,
- Edoardo Pasolli,
- Curtis Huttenhower,
- and Nicola Segata
Genome Res. April 2017 27: 626-638; Published in Advance February 6, 2017, doi:10.1101/gr.216242.116
..., but it is still difficult to characterize microbes in communities at the strain level. Metagenomic assembly (Nagarajan and Pop 2013) provides one solution and has been successful in identifying strains of uncharacterized species (Narasingarao et al. 2012; Brown et al. 2015). However, compared to assembling single...
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Method: Targeted genome fragmentation with CRISPR/Cas9 enables fast and efficient enrichment of small genomic regions and ultra-accurate sequencing with low DNA input (CRISPR-DS)
- Daniela Nachmanson,
- Shenyi Lian,
- Elizabeth K. Schmidt,
- Michael J. Hipp,
- Kathryn T. Baker,
- Yuezheng Zhang,
- Maria Tretiakova,
- Kaitlyn Loubet-Senear,
- Brendan F. Kohrn,
- Jesse J. Salk,
- Scott R. Kennedy,
- and Rosa Ana Risques
Genome Res. October 2018 28: 1589-1599; Published in Advance September 19, 2018, doi:10.1101/gr.235291.118
...important limitations that lead to nonoptimal sequencing outcomes, including uneven coverage, introduction of false mutations, and low recovery.The second major problem of NGS is the high error rate inherent to the sequencing process. Illumina currently offers the most accurate sequencing platform...
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Method: Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes
- Dirk D. Dolle,
- Zhicheng Liu,
- Matthew Cotten,
- Jared T. Simpson,
- Zamin Iqbal,
- Richard Durbin,
- Shane A. McCarthy,
- and Thomas M. Keane
Genome Res. February 2017 27: 300-309; Published in Advance December 16, 2016, doi:10.1101/gr.211748.116
...Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes Dirk D. Dolle 1 , 6 , Zhicheng Liu 1 , 2 , 6 , Matthew Cotten 1 , Jared T. Simpson 3 , 4 , Zamin Iqbal 5 , Richard Durbin...
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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
..., inevitably miss large parts of the genetic material one seeks to analyze. High-throughput sequencing or short-read sequencing (SRS), such as Illumina sequencing, has been routinely used in reference-based taxonomic classification of metagenomic data, which explains the development of many related tools...
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Resource: The western redcedar genome reveals low genetic diversity in a self-compatible conifer
- Tal J. Shalev,
- Omnia Gamal El-Dien,
- Macaire M.S. Yuen,
- Shu Shengqiang,
- Shaun D. Jackman,
- René L. Warren,
- Lauren Coombe,
- Lise van der Merwe,
- Ada Stewart,
- Lori B. Boston,
- Christopher Plott,
- Jerry Jenkins,
- Guifen He,
- Juying Yan,
- Mi Yan,
- Jie Guo,
- Jesse W. Breinholt,
- Leandro G. Neves,
- Jane Grimwood,
- Loren H. Rieseberg,
- Jeremy Schmutz,
- Inanc Birol,
- Matias Kirst,
- Alvin D. Yanchuk,
- Carol Ritland,
- John H. Russell,
- and Joerg Bohlmann
Genome Res. October 2022 32: 1952-1964; Published in Advance September 15, 2022, doi:10.1101/gr.276358.121
...expectations of genetic drift, suggestive of associative overdominance. Nonreference alleles at such loci often harbor deleterious mutations and are rare in natural populations, implying that balanced polymorphisms are maintained by linkage to dominant beneficial alleles. This may account for how WRC remains...
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