See online versions at

Tag Sequencing Protocol with Mock Community Description, from 2016. NOTE:THE COMBINATORIAL BARCODING AND INDEXING STRATEGY HERE IS SUITABLE FOR MISEQ AND HISEQ2500, BUT DUE TO HIGHER INCIDENCE OF INDEX HOPPING WITH NOVASEQ AND OTHER NEW PLATFORMS WITH PATTERNED FLOWCELLS, IT IS HIGHLY RECOMMENDED TO CHANGE TO UNIQUE DUAL INDEXING (UDI). This allows informatic removal of spurious forward-reverse combinations, resembling cross-contamination between samples (up to a few percent of sequences in our experience). We recommend replacing the forward and reverse barcodes/indices with unique 10 nt index combinations.

Filtering for cell collection

SangHoon Lee


Bacterial heterotrophic production

Jed Fuhrman


Molecular fingerprinting (ARISA)

SYBR Green I counts of viruses and bacteria


Rachel Noble / Anand Patel



Pulse field gel electrophoresis

DNA Extraction

Rohan Sachdeva; Cheryl Chow


Tutorial: Cytoscape-- Visualization of Microbial Networks


Cheryl Chow/ Jacob Cram