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Fig. 1 | Microbiome

Fig. 1

From: LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Fig. 1

Workflow of the LotuS2 pipeline. A LotuS2 can be installed either through (i) Bioconda, (ii) GitHub with the provided autoInstaller script, or (iii) using a Docker image. Alternatively, (iv) Galaxy web servers can also run LotuS2 (e.g., https://usegalaxy.eu/). B LotuS2 accepts amplicon reads from different sequencing platforms, along with a map file that describes barcodes, file locations, sample IDs, and other information. After demultiplexing and quality filtering, high-quality reads are clustered into either ASVs or OTUs. The optimal sequence representing each OTU/ASV is calculated in the seed extension step, where read pairs are also merged. Mid-quality reads are subsequently mapped onto these sequence clusters to increase cluster representation in abundance matrices. From OTU/ASV sequences, a phylogenetic tree is constructed, and each cluster is taxonomically assigned. These results are made available in multiple standard formats, such as tab-delimited files, .biom, or phyloseq objects to enable downstream analysis. New options in LotuS2 for each step are denoted with black colour whereas options in grey font were already available in LotuS

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