Removing primers

This step will remove primers from sequence read data. For that we will use QIIME with cutadapt plugin.

We will use the information from (Zackular et al. 2014) on forward and reverse primer used in sequencing. The following command remove primers from our dataset.

qiime cutadapt trim-paired \
--i-demultiplexed-sequences paired-end-demux.qza \
--p-front-f GTGYCAGCMGCCGCGGTAA \
--p-front-r GGACTACNVGGGTWTCTAAT \
--o-trimmed-sequences paired-end-demux-trimmed.qza"

References

Zackular, Joseph P, Mary AM Rogers, Mack T Ruffin IV, and Patrick D Schloss. 2014. “The Human Gut Microbiome as a Screening Tool for Colorectal Cancer.” Cancer Prevention Research 7 (11): 1112–21.