Decontam Processing

Filters out contanimants based on "prevalance method" from Decontam R package

Step 1.

Make a meta_table of the samples dictated as "Control" or "True" with column_name = "Sample_or_Control" Look at input for examples.

Step 2.

1. use Rscript scripts/decontam_process.R $path_output $path_otu $path_meta $dtype $threshold_interval $workers
   • dtype = "kraken", "xtree", "metaphlan", or taxa rank based on general abundance dataframe
   • threshold_interval = interval1,interval2
     • input as a tuple, seperator = ","
     • interval1 and interval2 are starting and ending points of seq(interval1,interval2, by = 5)

Outputs

Files/Figures
generates tsv file with new relative abundances based on filtering out specific taxa across different taxaonomic ranks
generates tsv file with taxa filtered out at specific thresholds
generates tsv file of threshold vs contaminated taxa
produces a figure of threshold vs contaminated taxa

EXAMPLE

Rscript scripts/decontam_process.R path/to/output_directory path/to/input/xtree/GTDB_.1_.05_c_metagenomics_ra.tsv path/to/input/xtree/df.meta.tsv xtree .1,.5 5


Rscript scripts/decontam_process.R /athena/masonlab/scratch/users/jaq4005/decontam_processing input/xtree/GTDB_.1_.05_c_metagenomics_ra.tsv input/xtree/df.meta.tsv xtree .1,.5 5