pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data

The pTrimmer was designed to handle multiple amplicon-sequencing (MAS) and target sequencing that have more than thousands pairs of primer sequence. The combination of k-mers and Needleman-Wunsch algorithm ensure its accuracy of primer trimming. We compared our method with the similar tools --cutPrimers, and found that our method have an improvement of 28.59% sensitivity and 11.87% specificity. The performance of pTrimmer is notably higher than existed tools that it is about 370 times faster than cutPrimers and even 17000 times faster than cutadapt per threads. Trimming 2158 pairs of primers from 11 million reads (Illumina PE 150bp) takes only 37 seconds and no more than 100 MB of memory consumption.