Knight Lab Admin Commands for Qiita. This is an Admin only plugin.

This plugin provides the following commands:

1. Sequence Processing Pipeline (SPP):

This command converts the BCL to FASTQ files, does adaptor and host/human sequence filtering, summarizes results and uploads the resulting files to Qiita as one or more new preparations and artifacts. This command is based on [mg-scripts](https://github.com/biocore/mg-scripts) and (metapool)[https://github.com/biocore/metagenomics_pooling_notebook/].

The new preparations that the SPP adds contain some automatically generated extra columns:

• raw_reads_r1r2: this is the total number of reads that the sequencing generated for R1 and R2.
• total_biological_reads_r1r2: the total of reads minus the adapters but before host/human filtering for R1 and R2.
• quality_filtered_reads_r1r2: total of reads that passed host/human filtering for R1 and R2.
• fraction_passing_quality_filter: the fraction of reads that are in quality_filtered_reads_r1r2 from the raw_reads_r1r2.