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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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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
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Commentary: Implications of the first complete human genome assembly Genome Res. April 2022 32: 595-598; Published in Advance March 31, 2022, doi:10.1101/gr.276723.122

...questions that perhaps can now be answered with the new complete assembly, especially in areas of their expertise, and why it is important from their academic perspectives.Can Alkan1: The complete assembly generated by the T2T Consortium has several implications in my research, namely algorithm development...
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Method: CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- Donovan H. Parks,
- Michael Imelfort,
- Connor T. Skennerton,
- Philip Hugenholtz,
- and Gene W. Tyson
Genome Res. July 2015 25: 1043-1055; Published in Advance May 14, 2015, doi:10.1101/gr.186072.114
...become impractical to finish all available reference s. Making robust biological inferences from draft s requires accurate estimates of their completeness and contamination. Current methods for assessing quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all...
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Resource: Recompleting the Caenorhabditis elegans genome
- Jun Yoshimura,
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Idan Gabdank,
- Lamia Wahba,
- Cheryl L. Smith,
- Mark L. Edgley,
- Ann E. Rougvie,
- Andrew Z. Fire,
- Shinichi Morishita,
- and Erich M. Schwarz
Genome Res. June 2019 29: 1009-1022; Published in Advance May 23, 2019, doi:10.1101/gr.244830.118
...to a megabase long (Jain et al. 2018a), and it seems likely that ultralong reads will become a key tool for completing eukaryotic s. Error rates of long reads do matter, however; we were able to do reliable liftover of gene annotations from N2 to VC2010 only because our PacBio reads gave us assemblies...
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Research: Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region
- Kiana Mohajeri,
- Stuart Cantsilieris,
- John Huddleston,
- Bradley J. Nelson,
- Bradley P. Coe,
- Catarina D. Campbell,
- Carl Baker,
- Lana Harshman,
- Katherine M. Munson,
- Zev N. Kronenberg,
- Milinn Kremitzki,
- Archana Raja,
- Claudia Rita Catacchio,
- Tina A. Graves,
- Richard K. Wilson,
- Mario Ventura,
- and Evan E. Eichler
Genome Res. November 2016 26: 1453-1467; Published in Advance October 7, 2016, doi:10.1101/gr.211284.116
...in the orangutan orthologous to REPD in humans was sequenced and assembled from 10 finished BAC clones and compared usingMiropeats (see Fig. 1, H2 for annotation). Lines connecting the two sequences indicate regions of homology and line colors highlight differences between the orangutan and human contig...
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Research: Global variability in gene expression and alternative splicing is modulated by mitochondrial content
- Raul Guantes,
- Alberto Rastrojo,
- Ricardo Neves,
- Ana Lima,
- Begoña Aguado,
- and Francisco J. Iborra
Genome Res. May 2015 25: 633-644; Published in Advance March 23, 2015, doi:10.1101/gr.178426.114
...Raul Guantes,1,7 Alberto Rastrojo,2,7 Ricardo Neves,3,6,7 Ana Lima,4 Begoña Aguado,2 and Francisco J. Iborra3,5 1Department of Condensed Matter Physics, Materials Science Institute “Nicolás Cabrera” and Institute of Condensed Matter Physics (IFIMAC), Universidad Autónoma de Madrid, Campus de...
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PERSPECTIVE: Against a Whole-Genome Shotgun
- Philip Green
Genome Res. May 1, 1997 7: 410-417; doi:10.1101/gr.7.5.410
...pilot study to test the approach. Variation within the implies that library representation for any selected region cannot necessarily be extrapolated to the as a whole. Moreover, most finishing problems scale poorly with the size of the region being sequenced (see below), implying that no matter how...
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COMMENTARY: Contemplating the End of the Beginning
- Francis S. Collins
Genome Res. May 1, 2001 11: 641-643; doi:10.1101/gr.1898
...were also scaling up production rapidly. An experiment carried out the preceding summer had documented the high degree of utility of a “working draft” human sequence; the half-dozen labs that compared draft and finished sequences found that the draft could answer most of the scientific queries...
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LETTER: Strategies and Tools for Whole-Genome Alignments
- Olivier Couronne,
- Alexander Poliakov,
- Nicolas Bray,
- Tigran Ishkhanov,
- Dmitriy Ryaboy,
- Edward Rubin,
- Lior Pachter,
- and Inna Dubchak
Genome Res. January 1, 2003 13: 73-80; doi:10.1101/gr.762503
...: 136 – 140 . ↵ Ma B. , Tromp J. , Li M. ( 2002 ) PatternHunter: Faster and more sensitive homology search. Bioinformatics 18 : 440 – 445 . ↵ Mardis E. , McPherson J. , Martienssen R. , Wilson R.K. , McCombie W.R. ( 2002 ) What is finished, and why does it matter. Genome Res. 12 : 669 – 671 . ↵ Mayor C...

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