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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
.... Moni-align uses a seed-and-extend strategy for aligning reads, utilizing maximal exact matches as seeds, which can be efficiently obtained with the r-index. Using both simulated and real short-read data sets, we demonstrate that Moni-align achieves alignment accuracy comparable to vg map and vg giraffe...
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Method: Memory-bound k-mer selection for large and evolutionarily diverse reference libraries
- Ali Osman Berk Şapcı and
- Siavash Mirarab
Genome Res. September 2024 34: 1455-1467; Published in Advance August 29, 2024, doi:10.1101/gr.279339.124
...of globally and eliminating the need to analyze all k-mers jointly at any point in library construction. Our highly optimized and flexible C++ implementation allowed us to compare several alternative strategies empirically. Our comprehensive results on taxonomic read classification and taxonomic profiling...
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Method: Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters
- Jens-Uwe Ulrich and
- Bernhard Y. Renard
Genome Res. June 2024 34: 914-924; Published in Advance June 17, 2024, doi:10.1101/gr.278623.123
...of bacteria, archaea, viruses, and fungi (Doytchinov and Dimov 2022). Over the past years, many tools have been developed that classify short and long sequencing reads by comparing their nucleotide sequences with a predefined set of references (Kim et al. 2016; Dilthey et al. 2019; Wood et al. 2019). Although...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...differences in the detection of fusion transcripts based on long- versus short-read sequencing. In these single-cell applications, the 10x Genomics single-cell sequencing libraries were based on 3′-end sequencing, inherently biasing sequencing coverage to the very 3′ ends of sequenced isoforms with Illumina...
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Method: Geometric deep learning framework for de novo genome assembly
- Lovro Vrček,
- Xavier Bresson,
- Thomas Laurent,
- Martin Schmitz,
- Kenji Kawaguchi,
- and Mile Šikić
Genome Res. April 2025 35: 839-849; Published in Advance October 29, 2024, doi:10.1101/gr.279307.124
...haploid s.De novo assembly provides essential insights into organism's biology and evolution by reconstructing its from short DNA fragments (or reads), without the access to the original genomic sequence. The assembly process is based on intricate methods on strings and graphs which were first introduced...
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Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...of evolutionary patterns relative to what could be obtained with access to a assembly (Freedman et al. 2021).Beginning with the advent of widespread access to high-throughput, low-cost short-read sequencing (Alkan et al. 2011) and continuing with recent technological advances in long-read DNA sequencing...
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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
...the raw HiFi read data back to the assembly to quantify the read coverage across the locus and validate this result. In a well-assembled region, the read coverage should be uniform, lacking sudden and dramatic changes in coverage in a short span. The sudden drop and rise in coverage and doubled coverage...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...methods to effectively differentiate technology errors from rare but real molecules. For annotation, we must agree on the strategy to capture molecular variability while still defining reference annotations that are useful for the genomics community.Long-read sequencing (LRS) technologies, such as those...
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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...of producing full-length transcripts, potentially providing a more complete representation of gene models than is obtained with short reads. However, challenges such as sequencing errors and library artifacts can compromise the reliability of long-read data. Initiatives like the LRGASP have demonstrated...
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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...Ciências, Universidade do Porto, 4169-007 Porto, Portugal; 3BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; 4Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark; 5Section...
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