Searching journal content for articles similar to Bzikadze et al. 32 (11-12): 2107.

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Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
...-quality assemblies can be created from xenic protist cultures by combining deep long-read sequencing with metagenomic assembly techniques, enabling rigorous comparative genomic analyses.ResultsCapturing Blastocystis diversityTo investigate the evolution of the Blastocystis genus, from its initial divergence through...
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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
...precisely genotype these long expansions (Mousavi et al. 2019). In contrast, modern long-read sequencing (LRS) technologies, like Oxford Nanopore Technologies (ONT) nanopore sequencing with newer chemistry or Pacific Biosciences (PacBio) high-fidelity circular consensus sequencing (HiFi), can give accurate...
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Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
- Rashid Al-Abri and
- Gamze Gürsoy
Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
.... This is also why it is difficult to assemble repetitive parts of s using short reads (Treangen and Salzberg 2012). ScatTR overcomes this challenge by using Monte Carlo sampling to efficiently find the best alignment to decoy references.Our results show that our approach enables accurate estimation of TR...
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Method: Highly accurate assembly polishing with DeepPolisher
- Mira Mastoras,
- Mobin Asri,
- Lucas Brambrink,
- Prajna Hebbar,
- Alexey Kolesnikov,
- Daniel E. Cook,
- Maria Nattestad,
- Julian Lucas,
- Taylor S. Won,
- Pi-Chuan Chang,
- Andrew Carroll,
- Benedict Paten,
- Kishwar Shafin,
- and and the Human Pangenome Reference Consortium
Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
...technologies contain errors that are not completely random but are influenced by biases toward different genomic features. Even using a consensus approach, recurrent errors in the reads can propagate into the assembly. Low complexity regions like homopolymers and tandem repeats are particularly challenging...
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Method: Accurate allocation of multimapped reads enables regulatory element analysis at repeats
- Alexis Morrissey,
- Jeffrey Shi,
- Daniela Q. James,
- and Shaun Mahony
Genome Res. June 2024 34: 937-951; Published in Advance July 10, 2024, doi:10.1101/gr.278638.123
...genomics analysis pipelines discard “multimapped” reads that align equally well to multiple genomic locations. Because multimapped reads arise predominantly from repeats, current analysis pipelines fail to detect a substantial portion of regulatory events that occur in repetitive regions. To address...
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Research: Optical genome mapping enables accurate testing of large repeat expansions
- Bart van der Sanden,
- Kornelia Neveling,
- Syukri Shukor,
- Michael D. Gallagher,
- Joyce Lee,
- Stephanie L. Burke,
- Maartje Pennings,
- Ronald van Beek,
- Michiel Oorsprong,
- Ellen Kater-Baats,
- Eveline Kamping,
- Alide A. Tieleman,
- Nicol C. Voermans,
- Ingrid E. Scheffer,
- Jozef Gecz,
- Mark A. Corbett,
- Lisenka E.L.M. Vissers,
- Andy Wing Chun Pang,
- Alex Hastie,
- Erik-Jan Kamsteeg,
- and Alexander Hoischen
Genome Res. April 2025 35: 810-823; Published in Advance March 20, 2025, doi:10.1101/gr.279491.124
...-based methods, although capable of -wide detection, are limited by inaccuracy (short-read technologies) and high associated costs (long-read technologies). This study evaluated optical mapping (OGM) as an efficient, accurate approach for measuring STR lengths and assessing somatic stability in 85 samples...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...(ONT), Hi-C, and RNA sequencing. For details, see the Supplemental Methods.Genome assembly and evaluationHigh-throughput Illumina data were employed for k-mer-based size estimation. PacBio HiFi and ONT ultralong reads were used to generate draft assemblies, whereas Hi-C data anchored contigs...
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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
...to difficulties in accurately recovering novel allele sequences with only short reads, and most of them would not even report those alleles. Genotyping with long reads may overcome this limitation as each gene sequence can be fully assembled before comparing with the Immuno Polymorphism Database (IPD), which...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...to be abundant in centromeric regions of many organisms and are essential for studying stability and evolutionary dynamics (Melters et al. 2013; Logsdon et al. 2024). To analyze tandem repeats, a critical step often involves the accurate reconstruction of the unit from either the assembled or unassembled (long...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...(coverage 0.1×–10×). For these five samples, complete major histocompatibility complex (MHC) haplotype sequences have been previously determined using long-read assembly (Houwaart et al. 2023). As our pan reference, we used a haplotype-resolved pan directed acyclic graph (DAG) of 49 MHC haplotype sequences...

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