PT  - JOURNAL ARTICLE
AU  - Yang Young Lu
AU  - Jiaxing Bai
AU  - Yiwen Wang
AU  - Ying Wang
AU  - Fengzhu Sun
TI  - CRAFT: Compact genome Representation towards large-scale Alignment-Free daTabase
AID  - 10.1101/2020.07.10.196741
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.07.10.196741
4099  - http://biorxiv.org/content/early/2020/07/12/2020.07.10.196741.short
4100  - http://biorxiv.org/content/early/2020/07/12/2020.07.10.196741.full
AB  - Motivation Rapid developments in sequencing technologies have boosted generating high volumes of sequence data. To archive and analyze those data, one primary step is sequence comparison. Alignment-free sequence comparison based on k-mer frequencies offers a computationally efficient solution, yet in practice, the k-mer frequency vectors for large k of practical interest lead to excessive memory and storage consumption.Results We report CRAFT, a general genomic/metagenomic search engine to learn compact representations of sequences and perform fast comparison between DNA sequences. Specifically, given genome or high throughput sequencing (HTS) data as input, CRAFT maps the data into a much smaller embedding space and locates the best matching genome in the archived massive sequence repositories. With 102 – 104-fold reduction of storage space, CRAFT performs fast query for gigabytes of data within seconds or minutes, achieving comparable performance as six state-of-the-art alignment-free measures.Availability CRAFT offers a user-friendly graphical user interface with one-click installation on Windows and Linux operating systems, freely available at https://github.com/jiaxingbai/CRAFT.Contact wangying{at}xmu.edu.cn; fsun{at}usc.eduSupplementary information Supplementary data are available at Bioinformatics online.Competing Interest StatementThe authors have declared no competing interest.