Nubeam-dedup: a fast and RAM-efficient tool to de-duplicate sequencing reads without mapping.
Journal Article (Journal Article)
SUMMARY: We present Nubeam-dedup, a fast and RAM-efficient tool to de-duplicate sequencing reads without reference genome. Nubeam-dedup represents nucleotides by matrices, transforms reads into products of matrices, and based on which assigns a unique number to a read. Thus, duplicate reads can be efficiently removed by using a collisionless hash function. Compared with other state-of-the-art reference-free tools, Nubeam-dedup uses 50-70% of CPU time and 10-15% of RAM. AVAILABILITY AND IMPLEMENTATION: Source code in C++ and manual are available at https://github.com/daihang16/nubeamdedup and https://haplotype.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Full Text
Duke Authors
Cited Authors
- Dai, H; Guan, Y
Published Date
- May 1, 2020
Published In
Volume / Issue
- 36 / 10
Start / End Page
- 3254 - 3256
PubMed ID
- 32091581
Electronic International Standard Serial Number (EISSN)
- 1367-4811
Digital Object Identifier (DOI)
- 10.1093/bioinformatics/btaa112
Language
- eng
Conference Location
- England