{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/viralvectors-compact-and-scalable-alignment","title":"ViralVectors: Compact and Scalable Alignment-free Virome Feature Generation","arxiv_id":"2304.02891","date":"2023-04-06","proceeding":null,"authors":["Sarwan Ali","Prakash Chourasia","Zahra Tayebi","Babatunde Bello","Murray Patterson"],"abstract":"The amount of sequencing data for SARS-CoV-2 is several orders of magnitude larger than any virus. This will continue to grow geometrically for SARS-CoV-2, and other viruses, as many countries heavily finance genomic surveillance efforts. Hence, we need methods for processing large amounts of sequence data to allow for effective yet timely decision-making. Such data will come from heterogeneous sources: aligned, unaligned, or even unassembled raw nucleotide or amino acid sequencing reads pertaining to the whole genome or regions (e.g., spike) of interest. In this work, we propose \\emph{ViralVectors}, a compact feature vector generation from virome sequencing data that allows effective downstream analysis. Such generation is based on \\emph{minimizers}, a type of lightweight \"signature\" of a sequence, used traditionally in assembly and read mapping -- to our knowledge, the first use minimizers in this way. We validate our approach on different types of sequencing data: (a) 2.5M SARS-CoV-2 spike sequences (to show scalability); (b) 3K Coronaviridae spike sequences (to show robustness to more genomic variability); and (c) 4K raw WGS reads sets taken from nasal-swab PCR tests (to show the ability to process unassembled reads). Our results show that ViralVectors outperforms current benchmarks in most classification and clustering tasks.","url_abs":"https://arxiv.org/abs/2304.02891v2","url_pdf":"https://arxiv.org/pdf/2304.02891v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"viralvectors-compact-and-scalable-alignment","repo_url":"https://github.com/slundberg/shap","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"tf","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"4k","task_name":"4k"},{"task_slug":"decision-making","task_name":"Decision Making"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}