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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
...of these notable repeat elements.Short tandem repeats (STRs), or microsatellites, are repetitive genomic elements found in both eukaryotes and prokaryotes in which a small motif, from 1 or 2 to 6–13 bp long (International Human Genome Sequencing Consortium 2001; Ellegren 2004; Chiu et al. 2021), is repeated...
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Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
...tools reveals that MotifScope can identify a greater number of motifs and more accurately represent the underlying repeat sequences. Moreover, MotifScope has been specifically designed to enable motif composition comparisons across assemblies of different individuals, as well as across long...
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Resource: Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR
- Wouter De Coster,
- Ida Höijer,
- Inge Bruggeman,
- Svenn D'Hert,
- Malin Melin,
- Adam Ameur,
- and Rosa Rademakers
Genome Res. November 2024 34: 2074-2080; Published in Advance August 15, 2024, doi:10.1101/gr.279265.124
...-Babu et al. 2024). A database of tandem repeat genotypes is beneficial to accurately assess an expanded allele's pathogenic potential versus a common population polymorphism, in which more common alleles are unlikely to be pathogenic for a patient with a rare disease. Recently, long-read sequencing...
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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
...with lengths that greatly exceed typical sequencing fragment sizes. When applied to data from the 1000 Genomes Project, ScatTR detects potential large TR expansions that other methods missed, highlighting its ability to better characterize -wide TR variation.Tandem repeats (TRs) are consecutively repeated...
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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
...accurately sequenced and annotated satellite repeats, segmental duplications, and repetitive regions more broadly. In combination with Allo's allocation of MMRs, the T2T may thus provide even greater abilities to map regulatory elements at repetitive regions of the .Together, the results of this work suggest...
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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
...was primarily used during the assembly stage. We plan to expand the DeepPolisher model to work on ONT reads in the future to address this fraction of errors. Around one-third of the residual errors lie in homopolymers and tandem repeats, sequences that are challenging even for highly accurate HiFi reads. We...
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Method: RAmbler resolves complex repeats in human Chromosomes 8, 19, and X
- Sakshar Chakravarty,
- Glennis Logsdon,
- and Stefano Lonardi
Genome Res. April 2025 35: 863-876; Published in Advance March 4, 2025, doi:10.1101/gr.279308.124
...to accurately reconstruct highly repetitive regions. In this work, we introduce RAmbler (Repeat Assembler), a reference-guided assembler specialized for the assembly of complex repetitive regions exclusively from Pacific Biosciences (PacBio) HiFi reads. RAmbler (1) identifies repetitive regions by detecting...
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Research: The motif composition of variable number tandem repeats impacts gene expression
- Tsung-Yu Lu,
- Paulina N. Smaruj,
- Geoffrey Fudenberg,
- Nicholas Mancuso,
- and Mark J.P. Chaisson
Genome Res. April 2023 33: 511-524; Published in Advance April 10, 2023, doi:10.1101/gr.276768.122
...); however, VNTR analysis with SRS suffers from ambiguity in read alignment, allelic bias of reference, and the hypermutability of repeat sequences. SNV and small indel variant calls from VNTR regions using short-read alignments are error-prone and blacklisted by ENCODE (Amemiya et al. 2019). Recently...
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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
...is because of a portion of the reads mapping to tandem repeat regions >10 bp. We could not calculate concordance rates for only the MHC-aligned reads because the true number of reads that should be mapped to this region is unknown. Although the alignments were highly concordant, this did not necessarily...
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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
...of the respective tests). Also, the read size of short-read sequencing methods has proven to be too limited to accurately detect all repeat expansions, and long-read sequencing is still not routinely used in most laboratories and is currently too expensive, while it allows the detection of an increasing amount...
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