Simple 16S pipeline running DADA2
YAMS16 requires R to be installed and will install the libraries that it needs if they aren't already. The db directory containing the SILVA 16S db should be kept in the same directory as the YAMS16.R script, which can be a different directory from where you are running it from.
Running YAMS16.R by itself gives the following info.
Usage: ./YAMS16.R [options]
Options: -a ADAPTER, --adapter=ADAPTER file of Illumina adapters (default: ./db/adapters/adapter.fasta)
-i INPUT, --input=INPUT
path of directory where fastq files are
-p PREFIX, --prefix=PREFIX
filename prefix name for project
-o OUTPUT, --output=OUTPUT
path where to output files (default .)
-t THREADS, --threads=THREADS
number of threads to use (default 1)
-x MAXLENGTH, --maxlength=MAXLENGTH
maximum amplicon length (default 240)
-n MINLENGTH, --minlength=MINLENGTH
minimum amplicon length (default 180)
-h, --help
Show this help message and exit
A typical usage would be something like
YAMS16.R -i fastq -p Project1 -t 16
This would run YAMS16 on the fastqs in directory fastq, set the project name to Project1, and use 16 threads.
When it finishes, it should generate several files
unit_table_LKT.tsv -- this is a table of LKT counts with columns being samples, rows being taxa taxa_16S_cons_LKT.tsv -- this is a table of taxonomic info with rows being taxa, columns being rank rep_set_LKT.fa -- this is a fasta file of the predicted amplicons from DADA2