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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
..., IGLV and TRBV retained high precision and recall even at the reduced coverage levels, with minimal changes observed. At 10× coverage, genotyping accuracy declined for certain loci, especially IGKV and IGHV, which demonstrated reduced recall compared with at 20× and 30× coverage. The TRDV locus...
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Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
- Nora Zidane,
- Carla Rodrigues,
- Valérie Bouchez,
- Martin Rethoret-Pasty,
- Virginie Passet,
- Sylvain Brisse,
- and Chiara Crestani
Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
...an alternative that offers benefits including real-time sequencing and cost efficiency, particularly useful in resource-limited settings. However, the historically higher error rates of ONT data have so far limited its application in high-precision genomic typing. The recent release of ONT's R10.4.1 chemistry...
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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...disease and complex traits but can be difficult to resolve with short-read sequencing. We present STRkit, a software package for genotyping STRs using long-read sequencing (LRS) that uses proximate single-nucleotide variants to improve genotyping accuracy without a priori haplotype information. We show...
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Method: AIDE: annotation-assisted isoform discovery with high precision
- Wei Vivian Li,
- Shan Li,
- Xin Tong,
- Ling Deng,
- Hubing Shi,
- and Jingyi Jessica Li
Genome Res. December 2019 29: 2056-2072; Published in Advance November 6, 2019, doi:10.1101/gr.251108.119
...is 10 × and the annotations have 40% purity (sets 1–3), the median precision rates of AIDE are as high as the third-quantile precision rates of Cufflinks. In addition, AIDE achieves high precision rates (> 75%) much more frequently than the other three methods (Fig. 2A). In terms of the recall rates...
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Method: High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing
- Nicholas D. Sanderson,
- Jeremy Swann,
- Leanne Barker,
- James Kavanagh,
- Sarah Hoosdally,
- Derrick Crook,
- The GonFast Investigators Group,
- Teresa L. Street,
- and David W. Eyre
Genome Res. September 2020 30: 1354-1363; Published in Advance September 1, 2020, doi:10.1101/gr.262865.120
..., with a coverage depth above 5×, suggested wild-type genotype (Supplemental Fig. S4).penA characterization using whole- and local de novo assembliesThe penA gene, associated with penicillin and ceftriaxone resistance, is a chromosomal antimicrobial resistance determinant with relatively high nucleotide sequence...
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Method: CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
- Marzia Rossato,
- Luca Marcolungo,
- Luca De Antoni,
- Giulia Lopatriello,
- Elisa Bellucci,
- Gaia Cortinovis,
- Giulia Frascarelli,
- Laura Nanni,
- Elena Bitocchi,
- Valerio Di Vittori,
- Leonardo Vincenzi,
- Filippo Lucchini,
- Kirstin E. Bett,
- Larissa Ramsay,
- David James Konkin,
- Massimo Delledonne,
- and Roberto Papa
Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
...CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant s Marzia Rossato1,2,6, Luca Marcolungo1,6, Luca De Antoni1, Giulia Lopatriello1, Elisa Bellucci3, Gaia Cortinovis3, Giulia Frascarelli3, Laura Nanni3, Elena Bitocchi3, Valerio Di Vittori3, Leonardo Vincenzi1, Filippo...
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Method: Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data
- Li Song,
- Gali Bai,
- X. Shirley Liu,
- Bo Li,
- and Heng Li
Genome Res. May 11, 2023 gr.277585.122; Published in Advance May 11, 2023, doi:10.1101/gr.277585.122
....8% of alleles found on the phased reference s (Figure 1C). While being highly sensitive, T1K also had high precision that about 95.0% of the called alleles can be validated in the phased s. The strategy of incorporating secondary read assignments with worse alignments in the intronic region improved...
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Method: HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay
- Jia Lv,
- Wenqian Jiao,
- Haobing Guo,
- Pingping Liu,
- Ruijia Wang,
- Lingling Zhang,
- Qifan Zeng,
- Xiaoli Hu,
- Zhenmin Bao,
- and Shi Wang
Genome Res. December 2018 28: 1919-1930; Published in Advance November 8, 2018, doi:10.1101/gr.235820.118
...Table S15). Genotyping concordance between technical replicates was 90.3%. When 10 loci with consistent calls between replicates were chosen for genotype validation by capillary electrophoresis, we found that all loci had the correct genotype calls (Fig. 5; Supplemental Table S15). This suggests...
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Method: Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors
- Nitan Shalon,
- David A. Relman,
- and Eitan Yaffe
Genome Res. May 2022 32: 986-1003; Published in Advance April 12, 2022, doi:10.1101/gr.275894.121
...).DiscussionWe present an algorithm that recovers all dominant cycles in a metagenomic assembly graph and reconstructs their corresponding s. Our implementation achieves high precision by combining graph theory and nucleotide-level vetting of cycles. We show that in the context of microbial communities...
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Method: Targeted genotyping of variable number tandem repeats with adVNTR
- Mehrdad Bakhtiari,
- Sharona Shleizer-Burko,
- Melissa Gymrek,
- Vikas Bansal,
- and Vineet Bafna
Genome Res. November 2018 28: 1709-1719; Published in Advance October 23, 2018, doi:10.1101/gr.235119.118
...in the AJ trio and obtained similar results (Supplemental Table S5).To test adVNTR for population-scale studies of VNTR genotypes using WGS data replacing labor-intensive gel electrophoresis (Cervera et al. 2007; Byrd and Manuck 2014), we scanned the PCR-free WGS data for 150 individuals (50 in each...

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