{"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/scalable-de-novo-genome-assembly-using-pregel","title":"Scalable De Novo Genome Assembly Using Pregel","arxiv_id":"1801.04453","date":"2018-01-13","proceeding":null,"authors":["Da Yan","Hongzhi Chen","James Cheng","Zhenkun Cai","Bin Shao"],"abstract":"De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables high-throughput genome sequencing and thus accelerates the discovery of new genomes. In this paper, we present a toolkit, called PPA-assembler, for de novo genome assembly in a distributed setting. The operations in our toolkit provide strong performance guarantees, and can be assembled to implement various sequencing strategies. PPA-assembler adopts the popular {\\em de Bruijn graph} based approach for sequencing, and each operation is implemented as a program in Google's Pregel framework for big graph processing. Experiments on large real and simulated datasets demonstrate that PPA-assembler is much more efficient than the state-of-the-arts and provides good sequencing quality.","url_abs":"http://arxiv.org/abs/1801.04453v1","url_pdf":"http://arxiv.org/pdf/1801.04453v1.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":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"scalable-de-novo-genome-assembly-using-pregel","repo_url":"https://github.com/yaobaiwei/PPA-Assembler","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"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}