Nubeam-dedup: a fast and RAM-efficient tool to de-duplicate sequencing reads without mapping.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 32091581.
- Also identified by DOI 10.1093/bioinformatics/btaa112.
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Abstract
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. Source code in C++ and manual are available at https://github.com/daihang16/nubeamdedup and https://haplotype.org. Supplementary data are available at Bioinformatics online.
Medical subject headings
- High-Throughput Nucleotide Sequencing
- Software