Shaopeng Liu

Sep 12, 2024 | onlinelibrary.wiley.com | Shaopeng Liu |Engineering Wuhan |Cheng Huang |Jin H. Han

Conflict of Interest The authors declare no conflict of interest. Supporting Information Filename Description smll202404639-sup-0001-SuppMat.docx6.2 MB Supporting Information smll202404639-sup-0002-MovieS1.mp4199.4 KB Supplemental Movie 1 smll202404639-sup-0003-MovieS2.mp45.1 MB Supplemental Movie 2 smll202404639-sup-0004-MovieS3.mp411.8 MB Supplemental Movie 3 References 1, , , , , , , , Nature 2022, 611, 485. 2, , , , Adv. Mater. 2018, 30, 1800561.

Apr 8, 2024 | biorxiv.org | Shaopeng Liu |David Koslicki

AbstractMotivation: Sketching methods provide scalable solutions for analyzing rapidly growing genomic data. A recent innovation in sketching methods, syncmers, has proven effective and has been employed for read alignment. Syncmers share fundamental features with the FracMinHash technique, a recent modification of the popular MinHash algorithm for set similarity estimation between sets of different sizes.

Mar 16, 2024 | biorxiv.org | Chunyu Ma |Shaopeng Liu |David Koslicki

AbstractMotivation: The sheer volume and variety of genomic content within microbial communities makes metagenomics a field rich in biomedical knowledge. To traverse these complex communities and their vast unknowns, metagenomic studies often depend on distinct reference databases, such as the Genome Taxonomy Database (GTDB), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), for various analytical purposes.

Dec 12, 2023 | biorxiv.org | Shaopeng Liu |David Koslicki

AbstractSketching methods provide scalable solutions for analyzing rapidly growing genomic data. A recent innovation in sketching methods, syncmers, has proven effective and has been employed for read alignment. Syncmers share fundamental features with the FracMinHash technique, a recent modification of the popular MinHash algorithm for set similarity estimation between sets of different sizes.

Nov 13, 2023 | biorxiv.org | Shaopeng Liu |David Koslicki

AbstractSketching methods provide scalable solutions for analyzing rapidly growing genomic data. A recent innovation in sketching methods, syncmers, has proven effective and has been employed for read alignment. Syncmers share fundamental features with the FracMinHash technique, a recent modification of the popular MinHash algorithm for set similarity estimation between sets of different sizes.