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Method: spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model
- Tianyu Liu,
- Tinglin Huang,
- Wengong Jin,
- Tinyi Chu,
- Rex Ying,
- and Hongyu Zhao
Genome Res. April 2026 36: 754-768; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
.... With imputation and denoising, we can obtain spatial transcriptomics with better coverage and more accurate gene expressions, which can facilitate downstream analyses.In this article, we have proposed spRefine, a reference-free imputation and denoising pipeline for spatial transcriptomic data analysis...
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Method: The Nubeam reference-free approach to analyze metagenomic sequencing reads
- Hang Dai and
- Yongtao Guan
Genome Res. September 2020 30: 1364-1375; Published in Advance September 3, 2020, doi:10.1101/gr.261750.120
...Hang Dai and Yongtao Guan Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina 27707, USA Corresponding authors: yongtao.guan@duke.edu, hang.dai@duke.eduAbstractWe present Nubeam (nucleotide be a matrix) as a novel reference-free approach...
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Method: Haplotype-aware sequence alignment to pangenome graphs
- Ghanshyam Chandra,
- Daniel Gibney,
- and Chirag Jain
Genome Res. September 2024 34: 1265-1275; Published in Advance July 16, 2024, doi:10.1101/gr.279143.124
...Haplotype-aware sequence alignment to pan graphs Ghanshyam Chandra1, Daniel Gibney2 and Chirag Jain1 1Department of Computational and Data Sciences, Indian Institute of Science, Bangalore Karnataka 560012, India; 2Department of Computer Science, The University of Texas at Dallas, Richardson, Texas...
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Method: RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes
- Ka Ming Nip,
- Readman Chiu,
- Chen Yang,
- Justin Chu,
- Hamid Mohamadi,
- René L. Warren,
- and Inanc Birol
Genome Res. August 2020 30: 1191-1200; Published in Advance August 17, 2020, doi:10.1101/gr.260174.119
...the aggregated sequencing data of multiple cells increases the complexity of the assembly problem.Reference-based assembly methods, such as StringTie (Pertea et al. 2015) and Scallop (Shao and Kingsford 2017), reconstruct transcripts based on the alignment of reads against the reference . Compared to reference-free...
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Method: Resolving the full spectrum of human genome variation using Linked-Reads
- Patrick Marks,
- Sarah Garcia,
- Alvaro Martinez Barrio,
- Kamila Belhocine,
- Jorge Bernate,
- Rajiv Bharadwaj,
- Keith Bjornson,
- Claudia Catalanotti,
- Josh Delaney,
- Adrian Fehr,
- Ian T. Fiddes,
- Brendan Galvin,
- Haynes Heaton,
- Jill Herschleb,
- Christopher Hindson,
- Esty Holt,
- Cassandra B. Jabara,
- Susanna Jett,
- Nikka Keivanfar,
- Sofia Kyriazopoulou-Panagiotopoulou,
- Monkol Lek,
- Bill Lin,
- Adam Lowe,
- Shazia Mahamdallie,
- Shamoni Maheshwari,
- Tony Makarewicz,
- Jamie Marshall,
- Francesca Meschi,
- Christopher J. O'Keefe,
- Heather Ordonez,
- Pranav Patel,
- Andrew Price,
- Ariel Royall,
- Elise Ruark,
- Sheila Seal,
- Michael Schnall-Levin,
- Preyas Shah,
- David Stafford,
- Stephen Williams,
- Indira Wu,
- Andrew Wei Xu,
- Nazneen Rahman,
- Daniel MacArthur,
- and Deanna M. Church
Genome Res. April 2019 29: 635-645; Published in Advance March 20, 2019, doi:10.1101/gr.234443.118
...molecule of origin.Improved and exome alignmentsSeveral improvements were made in the Long Ranger analysis pipeline to better take advantage of the Linked-Read data type. The first of these, the Lariat aligner (https://github.com/10XGenomics/lariat), expands on the “Read-Cloud” approach (Bishara et al...
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Method: scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment
- Zhitao Huang,
- Ruiqing Zheng,
- Pengzhen Jia,
- Xuhua Yan,
- Jinmiao Chen,
- and Min Li
Genome Res. February 2026 36: 387-396; Published in Advance January 20, 2026, doi:10.1101/gr.280410.125
...information. To achieve a balance between interomics alignment and intraomics heterogeneity, we propose a dual alignment strategy. Specifically, scSHEFT employs an anchor-based approach to align interomics anchor pairs and a contrastive-based strategy to preserve cellular heterogeneity within each omics layer...
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Method: TransRate: reference-free quality assessment of de novo transcriptome assemblies
- Richard Smith-Unna,
- Chris Boursnell,
- Rob Patro,
- Julian M. Hibberd,
- and Steven Kelly
Genome Res. August 2016 26: 1134-1144; Published in Advance June 1, 2016, doi:10.1101/gr.196469.115
...TransRate: reference-free quality assessment of de novo transcriptome assemblies Richard Smith-Unna 1 , Chris Boursnell 1 , Rob Patro 2 , Julian M. Hibberd 1 and Steven Kelly 3 1 Department of Plant Sciences, University...
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Method: Fast sequence alignment for centromeres with RaMA
- Pinglu Zhang,
- Yanming Wei,
- Qinzhong Tian,
- Quan Zou,
- and Yansu Wang
Genome Res. May 2025 35: 1209-1218; Published in Advance February 12, 2025, doi:10.1101/gr.279763.124
...to complex regions like centromeres, composed of extra-long tandem repeats (ETRs). However, a significant gap remains as current methodologies are inadequate for producing sequence alignments that effectively capture genetic events within ETRs, highlighting a pressing need for improved alignment tools...
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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
...Accurate short-read alignment through r-index-based pan indexing Rahul Varki1,4, Massimiliano Rossi1,4, Eddie Ferro1, Marco Oliva1, Erik Garrison2, Ben Langmead3 and Christina Boucher1 1Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida 32611...
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Method: Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes
- Dirk D. Dolle,
- Zhicheng Liu,
- Matthew Cotten,
- Jared T. Simpson,
- Zamin Iqbal,
- Richard Durbin,
- Shane A. McCarthy,
- and Thomas M. Keane
Genome Res. February 2017 27: 300-309; Published in Advance December 16, 2016, doi:10.1101/gr.211748.116
...Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes Dirk D. Dolle 1 , 6 , Zhicheng Liu 1 , 2 , 6 , Matthew Cotten 1 , Jared T. Simpson 3 , 4 , Zamin Iqbal 5 , Richard Durbin...

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