sequencing_prep_metagenomics: Function to produce files necessary to generate metagenomic...

In econtijoch/Biomass-Workflow: Microbial Density Data Generation and Analysis Tools

Description

Function to produce files necessary to generate metagenomic sequencing runs that utilizes the Beckmann robot for dilutions and creates sequencing mapping files in QIIME-ready format, from multiple experiment data sets.

Usage

sequencing_prep_metagenomics(experiment_data_list, n_barcode_plates,
  barcode_map_file = NULL, output_directory = getwd(), filter = T)

Arguments

experiment_data_list	an input list that contains the data from the samples you want to sequence (ideally, the output from DataAnalysis, or combinations of them)
n_barcode_plates	the number of barcode plates available (i.e. if you have 96 unique sequencing barcodes, this would be 1)
barcode_map_file	a string of the path to a file containing the barcode sequences, linker primer sequences, and barcode plate and well locations (see example data)
output_directory	OPTIONAL: a path to the directory for your desired output (Default = working directory)
filter	OPTIONAL: a boolean that indicates whether or not to filter out samples that have not passed the QC check from the DataAnalysis function (Default = TRUE)

Value

A list containing the data for as many sequencing runs necessary to sequence all of your samples. For each sequencing run, there will be a list of plates, corresponding to the data frames that contain the information necessary to use the Beckmann robot to dilute samples. There will also be a mapping file, and a list of samples included in that sequencing run.

econtijoch/Biomass-Workflow documentation built on May 15, 2019, 7:59 p.m.