Amplicon Sequence Analysis Pipeline (ASAP2)

Amplicon sequencing (16S rDNA, 18S rDNA, ITS etc.) has been widely used in microbial community studies. However, the data analysis remains complicated and lacks consistency.

Here, we developed an automatic pipeline, Amplicon Sequence Analysis Pipeline (ASAP2), to cover all the processes including data import, demultiplexing, read profile summarization, quality trimming, denoising, removing chimeric sequences, making feature (ASV) table using QIIME 2, Vegan and other tools.

The pipeline also automates the processes usually requiring manual user’s inspection such as detection of barcode orientation, selection of high-quality region of reads, and deciding resampling depth etc.

The outputs include taxonomic classification, alpha/beta diversity, community composition, ordination analysis and statistical tests (variable selection, CCA, RDA etc).

Multiple formats, including multiplexed or demultiplexed, paired-end or single-end, barcode inside or outside, raw or intermediate data (e.g. feature table), are accepted. More importantly, ASAP2 supports merging multiple sequencing runs which helps integrate and compare data from different sources (public databases and collaborators).

The pipeline minimizes hands-on interference and runs amplicon sequencing analysis automatically and consistently.