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.

This is an automated pipeline for analysis of shotgun metagenomic sequencing data. The results include taxonomic classification and functional classificatio (SEED, KEGG, COG and GO).
Below is the work flow:

• Quality evaluation
• Duplication removal
• Quality filtering
• Read statistics
• Format convert
• Assembly
• Data splitting
• DIAMOND search
• MEGAN classification
• 16/18S classification
• Table integration

Updated on Dec 11, 2018. More pipelines may be posted later.