作者
Po‐Yu Liu, Shan‐Hua Yang, Sung‐Yin Yang
发表日期
2022/3
期刊
Methods in Ecology and Evolution
卷号
13
期号
3
页码范围
560-568
简介
- Amplicon sequencing is widely implemented in microbiome‐associated studies. In recent years, microbial ecologists have switched to new algorithms for taxonomic identification and quantification. The amplicon sequence variant (ASV) denoising algorithm of unbiased sequence picking has replaced the OTU clustering methods. ASV can be used to detect and distinguish biological variations to the species OTU level (≥97% similarity). However, the ASV quantification among samples is sparse and less prevalent within the same batch.
- Here, we present a k‐mer based, alignment‐free algorithm—‘KTU’ (K‐mer Taxonomic Unit)—to iteratively re‐cluster ASVs into optimal biological taxonomic units.
- The ‘KTU’ algorithm comprises four parts: (a) The k‐mer frequency calling is sliding window counted by tetranucleotide frequencies from both ends of the DNA sequence. (b) The similarities in k‐mer frequencies among …
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PY Liu, SH Yang, SY Yang - Methods in Ecology and Evolution, 2022