Primer Trimming

We start by trimming off primers, barcodes, and illumina adapters using the Cutadapt software. The primer sequences are read in from the primer_data.csv file. For each file, we detect what primer was used using the file name (see further documentation here), and then use the following command to trim primers using Cutadapt:

${CUTADAPT} -g ${MFU_F} \
     -G "${MFU_R}" \
     -o ../for_dada2/${R1} \
     -p ../for_dada2/${R2} \
    --discard-untrimmed \
    -j 0 \
"${R1}" "${R2}" 1> "../cutadapt_reports/${FILE_NAME}_trim_report.txt"

Flag	Meaning
-g	sequence of the forward primer
-G	sequence of the reverse primer
-o	output location of forward fastq file
-p	output location of reverse fastq file
--discard-untrimmed	discard sequences where the primer is not found
-j	automatically detect the number of available cores