Methods
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
Filtration.pdf
Bacterial heterotrophic production
Jed Fuhrman
Production.pdf
Molecular fingerprinting (ARISA)
SYBR Green I counts of viruses and bacteria
Rachel Noble / Anand Patel
SYBRGreen.pdf
SYBR_Green_Extended.pdf
Pulse field gel electrophoresis
John Griffith
PulseFieldElectrophoresis.pdf
DNA Extraction
Rohan Sachdeva; Cheryl Chow
Tutorial: Cytoscape-- Visualization of Microbial Networks
Cytoscape_Tutorial_-_STAMPS.pdf
Cheryl Chow/ Jacob Cram