ASAP pipeline

Amplicon Sequence Analysis Pipeline (ASAP 1.4, May 2018)

This is an automated pipeline for analysis of amplicon sequence data (could be multiple sequencing runs) including 16S, 18S and ITS.

It wraps QIIME commands and complements them with additional analysis where QIIME is not good at, such as combine multiple sequencing runs, OTU clustering and chimeric removal with UPARSE, alignment filtering with Gblock, removing Chloroplast sequences.

The results include OTU sequences, OTU table, taxonomic classification, community composition charts, PCoA charts (UniFrac, Bray Curtis ...), Alpha diversity indexes (OTU number, Shannon, Chao1, Goods Coverage, PD_whole, Simposon ...), rarefaction curve, and processed Fastq files for submission to NCBI.

Below is the work flow:

For more information, see the slides.   To analyze your data, go to Job Submission.